Small molecule ire1-alpha inhibitors

ABSTRACT

Described herein are IRE1α inhibitors, compositions containing such inhibitors, and methods of treatment that include administration of such compounds. Exemplary compounds are provided throughout the application.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.16/116,065, filed Aug. 29, 2018, which is a continuation of U.S. patentapplication Ser. No. 15/449,547, filed Mar. 3, 2017, which claims thebenefit under 35 U.S.C. § 119(e) of U.S. Provisional Patent ApplicationSer. No. 62/303,951, filed Mar. 4, 2016, and of U.S. Provisional PatentApplication Ser. No. 62/303,236, filed Mar. 3, 2016, the disclosures ofboth of which are incorporated herein in their entirety by reference.

BACKGROUND

Aggressive tumors have evolved strategies that enable them to thriveunder constant adverse conditions. Cancer cells respond to hypoxia,nutrient starvation, oxidative stress, and high metabolic demand byadjusting their protein folding capacity via the endoplasmic reticulum(ER) stress response pathway. Cancer patients would benefit from thedevelopment of new strategies and therapeutics.

SUMMARY

Described herein are IRE1α inhibitors, compositions containing suchinhibitors, and methods of treatment that include administration of suchcompounds.

The inventors have discovered that XBP1 can promote tumor progression byconfounding the development of protective antitumor immunity in theovarian cancer tumor microenvironment. Without XBP1, tumor residentdendritic cells fail to accumulate intracellular lipids, which normallydisrupt effective antigen cross-presentation. This pathological lipidaccumulation is fundamentally driven by reactive oxygen species-mediatedlipid peroxidation, which directly destabilizes protein-foldingchaperones within the endoplasmic reticulum to induce a state of ERstress and XBP1 activation. Additionally, the inventors have found thatIRE1α-mediated XBP1 signaling is involved in myeloid cell production ofimmunosuppressive prostaglandins such as prostaglandin E2 (PGE2).

These findings have led to the development of novel small-molecule IRE1αinhibitors with the ability to induce two parallel and mutuallyreinforcing anti-tumor mechanisms, namely the direct inhibition of tumorgrowth and the simultaneous induction of robust anti-tumor immunity.Such a compound is highly desirable, as no effective, targeted therapiescurrently exist for either TNBC or ovarian cancer.

Described herein are novel IRE1α kinase inhibitors that exhibit suchimmune-modulatory properties and/or that allosterically block IRE1alphaendoribonuclease function. The identified direct IRE1α inhibitors haveunique chemical structures, unique binding mechanisms, inhibitoryactivity, and off-target effects.

One aspect of the invention is a compound of formula I:

wherein:

-   -   A and B are separately each a heterocyclyl ring or a phenyl        group, where the A ring has x R₁ substituents;    -   C is phenyl or pyridinyl;    -   D is heterocyclyl ring;    -   linkage₁ is a single bond between A and B;    -   linkage₂ is a C₁-C₃ alkylamido, amidoalkyl, amino, urea,        alkylurea, or ureaalkyl with a first and second terminal atom;    -   y is an integer of 0-3, and when y is 0, the linkage between the        rings is a single bond;    -   x is an integer of 0-4;    -   v is an integer of 0-2;    -   R₁ substituents on the A ring are selected from amino,        optionally substituted C₁-C₄ alkyl, optionally substituted        ether, optionally substituted C₁-C₄ alkoxy, oxy, hydroxy,        —NH—SO₂-phenyl-(R₅), and cyano;    -   R₂ substituents on the B ring are selected from amino, and        optionally substituted C₁-C₄ alkyl;    -   R₃ substituents on the C ring are selected from halo, CF₃,        optionally substituted C₁-C₄ alkyl, and optionally substituted        heteroaryl; and    -   R₄ substituents on the D ring are selected from optionally        substituted C₁-C₄ alkyl, optionally substituted C₁-C₄ alkoxy,        (optionally substituted C₁-C₄ alkylene)-OH, hydroxy, optionally        substituted aryl, optionally substituted benzyl, and optionally        substituted benzaldehyde;    -   R₅ is halo; or    -   a pharmaceutically acceptable salt thereof.

Another aspect of the invention is compound selected from any of thecompounds in Tables 1-4, the Examples or a pharmaceutically acceptablesalt thereof.

Another aspect of the invention is a composition that includes a carrierand any of the compounds of formula I, pharmaceutically acceptable saltsthereof, or any combination of such compounds.

Another aspect of the invention is a composition that includes a carrierand any of the compounds in the Examples, pharmaceutically acceptablesalts thereof, or any combination thereof.

Another aspect of the invention is a method that includes administeringone or more of such compositions to a mammal. For example, the mammalcan be in need of administration of the composition. Such a mammal can,for example, have cancer, a neurodegenerative disease, inflammation, ametabolic disorder, liver dysfunction, brain ischemia, heart ischemia,or an autoimmune disease such as systemic lupus erythematosus. In somecases, the mammal has triple negative breast cancer or ovarian cancer.

The compositions and methods described herein can include one or moreagents such as vitamin E, an antioxidant, and/or hydralazine. Suchagents can sequester lipid peroxidation byproducts, and can be effectivetreatments for controlling ER stress responses and sustained IRE1α/XBP1signaling in tumor-associated dendritic cells exposed, for example, toovarian cancer-derived ascites.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A is the structure of vitamin E (VitE).

FIG. 1B is the structure of hydralazine (Hlz), a representative memberof lipid peroxidation-sequestering hydrazines.

FIG. 1C is RT-qPCR analyses of markers of ER stress after culturingpurified tumor-resident DCs in the absence (grey bars) or presence(green bars) of 25% cell-free ovarian cancer ascites supernatants for 18hours. Data are normalized to Actb expression in each sample.

FIG. 1D is flow cytometry analysis of lipid accumulation in mouse bonemarrow-derived dendritic cells exposed to the indicated treatments,measured by BODIPY 493/503 staining intensity. Both raw data andquantified geometric mean fluorescence intensity (MFI) are shown.

FIG. 2A is a cartoon of a cleavable RNA probe and IRE1α-dependenthairpin cleavage site. In FIG. 2A, the quenching dye is released,fluorescence is emitted.

FIG. 2B is a cartoon of a point mutation (G→C) in the hairpin thatabrogates IRE1α activity against RNA probe, controlling forcontamination by non-specific RNAses. In FIG. 2B, the quenching dye isretained, and no fluorescence is emitted.

FIG. 3 is the structure of an IRE1α inhibitor identified bycomputational screening and confirmed by human IRE1α FRET assay(commercially available from InterBioScreen).

DETAILED DESCRIPTION

The invention relates to compounds that can modulate the activity ofIRE1α. IRE1α is a type I transmembrane protein with dual enzymaticactivities, including an N-terminal domain that projects into theluminal side of the endoplasmic reticulum (IRE1-LD) and aserine/threonine kinase domain plus a C-terminal ribonuclease (RNase)domain located on the cytosolic side of the protein.

The compounds of the invention include any of the compounds describedherein, in the Examples, the figures, and Tables 1-4. Embodiments of theinvention include but are not limited to one or more compounds offormula I:

wherein:

-   -   A and B are separately each a heterocyclyl ring or a phenyl        group, where the A ring has x R₁ substituents;    -   C is phenyl or pyridinyl;    -   D is heterocyclyl ring;    -   linkage₁ is a single bond between A and B;    -   linkage₂ is a C₁-C₃ alkylamido, amidoalkyl, amino, urea,        alkylurea, or ureaalkyl with a first and second terminal atom;    -   y is an integer of 0-3, and when y is 0, the linkage between the        rings is a single bond;    -   x is an integer of 0-4;    -   v is an integer of 0-2;    -   R₁ substituents on the A ring are selected from amino,        optionally substituted C₁-C₄ alkyl, optionally substituted        ether, optionally substituted C₁-C₄ alkoxy, oxy, hydroxy,        —NH—SO₂-phenyl-(R₅), and cyano;    -   R₂ substituents on the B ring are selected from amino, and        optionally substituted C₁-C₄ alkyl;    -   R₃ substituents on the C ring are selected from halo, CF₃,        optionally substituted C₁-C₄ alkyl, and optionally substituted        heteroaryl; and    -   R₄ substituents on the D ring are selected from optionally        substituted C₁-C₄ alkyl, optionally substituted C₁-C₄ alkoxy,        (optionally substituted C₁-C₄ alkylene)-OH, hydroxy, optionally        substituted aryl, optionally substituted benzyl, and optionally        substituted benzaldehyde;    -   R₅ is halo; or    -   a pharmaceutically acceptable salt thereof.

All structures encompassed within a claim are “chemically feasible”, bywhich is meant that the structure depicted by any combination orsubcombination of optional substituents meant to be recited by the claimis physically capable of existence with at least some stability as canbe determined by the laws of structural chemistry and byexperimentation. Structures that are not chemically feasible are notwithin a claimed set of compounds.

When a substituent is specified to be an atom or atoms of specifiedidentity, “or a bond”, a configuration is referred to when thesubstituent is “a bond” that the groups that are immediately adjacent tothe specified substituent are directly connected to each other by achemically feasible bonding configuration.

In general, “optionally substituted” and “substituent” refers to anorganic group as defined herein in which one or more bonds to a hydrogenatom contained therein are optionally replaced by one or more bonds to anon-hydrogen atom such as, but not limited to, a halogen (i.e., “halo”selected from F, Cl, Br, and I); an oxygen atom in groups such ashydroxyl groups, alkoxy groups, aryloxy groups, aralkyloxy groups,oxo(carbonyl) groups, carboxyl groups including carboxylic acids,carboxylates, and carboxylate esters; a sulfur atom in groups such asthiol groups, alkyl and aryl sulfide groups, sulfoxide groups, sulfonegroups, sulfonyl groups, and sulfonamide groups; a nitrogen atom ingroups such as amines, hydroxylamines, nitriles, nitro groups. N-oxides,hydrazides, azides, and enamines; and other heteroatoms in various othergroups. Non-limiting examples of substituents that can be bonded to asubstituted carbon (or other) atom include F, Cl, Br, I, OR′,OC(O)N(R′)₂, CN, CF₃, OCF₃, R′, O, S, C(O), S(O), methylenedioxy,ethylenedioxy, N(R′)₂, SR′, SOR′, SO₂R′, SO₂N(R′)₂, SO₃R′, C(O)R′,C(O)C(O)R′, C(O)CH₂C(O)R′, C(S)R′, C(O)OR′, OC(O)R′, C(O)N(R′)₂,OC(O)N(R′)₂, C(S)N(R′)₂, (CH₂)₀₋₂NHC(O)R′, (CH₂)₀₋₂N(R′)N(R′)₂,N(R′)N(R′)C(O)R′, N(R′)N(R′)C(O)OR′, N(R′)N(R′)CON(R′)₂, N(R′)SO₂R′,N(R′)SO₂N(R′)₂, N(R′)C(O)OR′, N(R′)C(O)R′. N(R′)C(S)R′, N(R′)C(O)N(R′)₂,N(R′)C(S)N(R′)₂, N(COR′)COR′, N(OR′)R′, C(═NH)N(R′)₂, C(O)N(OR′)R′, orC(═NOR′)R′ wherein R′ can be hydrogen or a carbon-based moiety, andwherein the carbon-based moiety can itself be further substituted. Insome cases the R′ group is a hydrogen, C₁-C₆ alkyl, or phenyl.

In many of the compounds described herein, the optional substituents areselected from amino, C₁-C₃ alkyl, ether, alkoxy, oxy, CF₃, and cyanoC₁-C₃ alkoxy, benzyl, and benzaldehyde. The ether and alkoxy groups canhave 1-6 carbon atoms.

Substituted alkyl, alkenyl, alkynyl, cycloalkyl, and cycloalkenyl groupsas well as other substituted groups also include groups in which one ormore bonds to a hydrogen atom are replaced by one or more bonds,including double or triple bonds, to a carbon atom, or to a heteroatomsuch as, but not limited to, oxygen in carbonyl (oxo), carboxyl, ester,amide, imide, urethane, and urea groups; and nitrogen in imines,hydroxyimines, oximes, hydrazones, amidines, guanidines, and nitriles.

Substituted ring groups such as substituted aryl, heterocyclyl andheteroaryl groups also include rings and fused ring systems in which abond to a hydrogen atom is replaced with a bond to a carbon atom.Therefore, substituted aryl, heterocyclyl and heteroaryl groups can alsobe substituted with alkyl, alkenyl, cycloalkyl, aryl, heteroaryl, andalkynyl groups as defined herein, which can themselves be furthersubstituted.

The term “heteroatoms” as used herein refers to non-carbon andnon-hydrogen atoms, capable of forming covalent bonds with carbon, andis not otherwise limited. Typical heteroatoms are N, O, and S. Whensulfur (S) is referred to, it is understood that the sulfur can be inany of the oxidation states in which it is found, thus includingsulfoxides (R—S(O)—R′) and sulfones (R—S(O)₂—R′), unless the oxidationstate is specified; thus, the term “sulfone” encompasses only thesulfone form of sulfur; the term “sulfide” encompasses only the sulfide(R—S—R′) form of sulfur. When the phrases such as “heteroatoms selectedfrom the group consisting of O, NH, NR′ and S,” or “[variable] is O, S .. . ” are used, they are understood to encompass all of the sulfide,sulfoxide and sulfone oxidation states of sulfur.

Alkyl groups include straight chain and branched alkyl groups andcycloalkyl groups having from 1 to about 20 carbon atoms, and typicallyfrom 1 to 12 carbons or, in some embodiments, from 1 to 8 carbon atoms.Examples of straight chain alkyl groups include those with from 1 to 8carbon atoms such as methyl, ethyl, n-propyl, n-butyl, n-pentyl,n-hexyl, n-heptyl, and n-octyl groups. Examples of branched alkyl groupsinclude, but are not limited to, isopropyl, isobutyl, sec-butyl,t-butyl, neopentyl, isopentyl, and 2,2-dimethylpropyl groups.Representative substituted alkyl groups can be substituted one or moretimes with any of the groups listed above, for example, amino, hydroxy,cyano, carboxy, nitro, thio, alkoxy, and halogen groups.

An “alkylene” group refers to a divalent alkyl radical. Any of the abovementioned monovalent alkyl groups may be an alkylene by abstraction of asecond hydrogen atom from the alkyl. In some embodiments, an alkylene isa C₁-C₆alkylene. In some embodiments, an alkylene is a C₁-C₃alkylene.Examples of alkylene groups include, but are not limited to, —CH₂—,—CH₂CH₂—, —CH₂CH₂CH₂—, —CH₂CH₂CH₂CH₂—, and the like.

Cycloalkyl groups are alkyl groups forming a ring structure, which canbe substituted or unsubstituted. Examples of cycloalkyl include, but arenot limited to, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl,cycloheptyl, and cyclooctyl groups. In some embodiments, the cycloalkylgroup has 3 to 8 ring members, whereas in other embodiments the numberof ring carbon atoms range from 3 to 5, 3 to 6, or 3 to 7. Cycloalkylgroups further include polycyclic cycloalkyl groups such as, but notlimited to, norbornyl, adamantyl, bornyl, camphenyl, isocamphenyl, andcarenyl groups, and fused rings such as, but not limited to, decalinyl,and the like. Cycloalkyl groups also include rings that are substitutedwith straight or branched chain alkyl groups as defined above.Representative substituted cycloalkyl groups can be mono-substituted orsubstituted more than once, such as, but not limited to, 2,2-, 2,3-,2,4-2,5- or 2,6-disubstituted cyclohexyl groups or mono-, di- ortri-substituted norbornyl or cycloheptyl groups, which can besubstituted with, for example, amino, hydroxy, cyano, carboxy, nitro,thio, alkoxy, and halogen groups.

The terms “carbocyclic” and “carbocycle” denote a ring structure whereinthe atoms of the ring are carbon. In some embodiments, the carbocyclehas 3 to 8 ring members, whereas in other embodiments the number of ringcarbon atoms is 4, 5, 6, or 7. Unless specifically indicated to thecontrary, the carbocyclic ring can be substituted with as many as Nsubstituents wherein N is the size of the carbocyclic ring with forexample, amino, hydroxy, cyano, carboxy, nitro, thio, alkoxy, andhalogen groups.

(Cycloalkyl)alkyl groups, also denoted cycloalkylalkyl, are alkyl groupsas defined above in which a hydrogen or carbon bond of the alkyl groupis replaced with a bond to a cycloalkyl group as defined above.

Alkenyl groups include straight and branched chain and cyclic alkylgroups as defined above, except that at least one double bond existsbetween two carbon atoms. Thus, alkenyl groups have from 2 to about 20carbon atoms, and typically from 2 to 12 carbons or, in someembodiments, from 2 to 8 carbon atoms. Examples include, but are notlimited to —CH═CH(CH₃), —CH═C(CH₃)₂, —C(CH₃)═CH₂, —C(CH₃)═CH(CH₃).—C(CH₂CH₃)═CH₂, vinyl, cyclohexenyl, cyclopentenyl, cyclohexadienyl,butadienyl, pentadienyl, and hexadienyl among others.

The term “cycloalkenyl” alone or in combination denotes a cyclic alkenylgroup wherein at least one double bond is present in the ring structure.Cycloalkenyl groups include cycloalkyl groups having at least one doublebond between two adjacent carbon atoms. Thus for example, cycloalkenylgroups include but are not limited to cyclohexenyl, cyclopentenyl, andcyclohexadienyl groups.

(Cycloalkenyl)alkyl groups are alkyl groups as defined above in which ahydrogen or carbon bond of the alkyl group is replaced with a bond to acycloalkenyl group as defined above.

Alkynyl groups include straight and branched chain alkyl groups, exceptthat at least one triple bond exists between two carbon atoms. Thus,alkynyl groups have from 2 to about 20 carbon atoms, and typically from2 to 12 carbons or, in some embodiments, from 2 to 8 carbon atoms.Examples include, but are not limited to —C≡CH, —C≡C(CH₃), —C≡C(CH₂CH₃),—CH₂C≡CH, —CH₂C≡C(CH₃), and —CH₂C≡C(CH₂CH₃), among others.

Aryl groups are cyclic aromatic hydrocarbons that do not containheteroatoms. Thus aryl groups include, but are not limited to, phenyl,azulenyl, heptalenyl, biphenyl, indacenyl, fluorenyl, phenanthrenyl,triphenylenyl, pyrenyl, naphthacenyl, chrysenyl, biphenylenyl,anthracenyl, and naphthyl groups. In some embodiments, aryl groupscontain 6-14 carbons in the ring portions of the groups. The phrase“aryl groups” includes groups containing fused rings, such as fusedaromatic-aliphatic ring systems (e.g., indanyl, tetrahydronaphthyl, andthe like), and also includes substituted aryl groups that have othergroups, including but not limited to alkyl, halo, amino, hydroxy, cyano,carboxy, nitro, thio, or alkoxy groups, bonded to one of the ring atoms.Representative substituted aryl groups can be mono-substituted orsubstituted more than once, such as, but not limited to, 2-, 3-, 4-, 5-,or 6-substituted phenyl or naphthyl groups, which can be substitutedwith groups including but not limited to those listed above.

Aralkyl groups are alkyl groups as defined above in which a hydrogen orcarbon bond of an alkyl group is replaced with a bond to an aryl groupas defined above. Representative aralkyl groups include benzyl andphenylethyl groups and fused (cycloalkylaryl)alkyl groups such as4-ethyl-indanyl. The aryl moiety or the alkyl moiety or both areoptionally substituted with other groups, including but not limited toalkyl, halo, amino, hydroxy, cyano, carboxy, nitro, thio, or alkoxygroups. Aralkenyl group are alkenyl groups as defined above in which ahydrogen or carbon bond of an alkyl group is replaced with a bond to anaryl group as defined above.

Heterocyclyl groups include aromatic and non-aromatic ring compoundscontaining 3 or more ring members, of which one or more is a heteroatomsuch as, but not limited to, N, O. S, or P. Heteroaryl andheterocyclicalkyl groups are included in the definition of heterocyclyl.In some embodiments, heterocyclyl groups include 3 to 20 ring members,whereas other such groups have 3 to 15 ring members. At least one ringcontains a heteroatom, but every ring in a polycyclic system need notcontain a heteroatom. For example, a dioxolanyl ring and abenzdioxolanyl ring system (methylenedioxyphenyl ring system) are bothheterocyclyl groups within the meaning herein. A heterocyclyl groupdesignated as a C₂-heterocyclyl can be a 5-ring with two carbon atomsand three heteroatoms, a 6-ring with two carbon atoms and fourheteroatoms and so forth. Likewise a C-heterocyclyl can be a 5-ring withone heteroatom, a 6-ring with two heteroatoms, and so forth. The numberof carbon atoms plus the number of heteroatoms sums up to equal thetotal number of ring atoms. In some cases, the heterocyclyl is a singlering. In other cases, the heterocyclyl is a fusion of two or threerings. The phrase “heterocyclyl group” includes fused ring speciesincluding those having fused aromatic and non-aromatic groups. Thephrase also includes polycyclic ring systems containing a heteroatomsuch as, but not limited to, quinuclidyl and also includes heterocyclylgroups that have substituents, including but not limited to alkyl, halo,amino, hydroxy, cyano, carboxy, nitro, thio, or alkoxy groups, bonded toone of the ring members. A heterocyclyl group as defined herein can be aheteroaryl group or a partially or completely saturated cyclic groupincluding at least one ring heteroatom. Heterocyclyl groups include, butare not limited to, pyrrolidinyl, furanyl, tetrahydrofuranyl,dioxolanyl, piperidinyl, piperazinyl, morpholinyl, pyrrolyl, pyrazolyl,triazolyl, tetrazolyl, oxazolyl, isoxazolyl, thiazolyl, pyridinyl,thiophenyl, benzothiophenyl, benzofuranyl, dihydrobenzofuranyl, indolyl,dihydroindolyl, azaindolyl, indazolyl, benzimidazolyl,azabenzimidazolyl, benzoxazolyl, benzothiazolyl, benzothiadiazolyl,imidazopyridinyl, isoxazolopyridinyl, thianaphthalenyl, purinyl,xanthinyl, adeninyl, guaninyl, quinolinyl, isoquinolinyl,tetrahydroquinolinyl, quinoxalinyl, and quinazolinyl groups.Heterocyclyl groups can be substituted. Representative substitutedheterocyclyl groups can be mono-substituted or substituted more thanonce, including but not limited to, rings containing at least oneheteroatom which are mono, di, tri, tetra, penta, hexa, orhigher-substituted with substituents such as those listed above,including but not limited to alkyl, halo, amino, hydroxy, cyano,carboxy, nitro, thio, and alkoxy groups.

Heteroaryl groups are aromatic ring compounds containing 5 or more ringmembers, of which, one or more is a heteroatom such as, but not limitedto, N, O, and S. A heteroaryl group designated as a C₂-heteroaryl can bea 5-ring with two carbon atoms and three heteroatoms, a 6-ring with twocarbon atoms and four heteroatoms and so forth. Likewise a C₄-heteroarylcan be a 5-ring with one heteroatom, a 6-ring with two heteroatoms, andso forth. The number of carbon atoms plus the number of heteroatoms sumsup to equal the total number of ring atoms. Heteroaryl groups include,but are not limited to, groups such as pyrrolyl, pyrazolyl, triazolyl,tetrazolyl, oxazolyl, isoxazolyl, thiazolyl, pyridinyl, thiophenyl,benzothiophenyl, benzofuranyl, indolyl, azaindolyl, indazolyl,benzimidazolyl, azabenzimidazolyl, benzoxazolyl, benzothiazolyl,benzothiadiazolyl, imidazopyridinyl, isoxazolopyridinyl,thianaphthalenyl, purinyl, xanthinyl, adeninyl, guaninyl, quinolinyl,isoquinolinyl, tetrahydroquinolinyl, tetrahydroisoquinolinyl,quinoxalinyl, and quinazolinyl groups. The terms “heteroaryl” and“heteroaryl groups” include fused ring compounds such as wherein atleast one ring, but not necessarily all rings, are aromatic, includingtetrahydroquinolinyl, tetrahydroisoquinolinyl, indolyl and 2,3-dihydroindolyl. The term also includes heteroaryl groups that have other groupsbonded to one of the ring members, including but not limited to alkyl,halo, amino, hydroxy, cyano, carboxy, nitro, thio, or alkoxy groups.Representative substituted heteroaryl groups can be substituted one ormore times with groups such as those listed above.

Additional examples of aryl and heteroaryl groups include but are notlimited to phenyl, biphenyl, indenyl, naphthyl (1-naphthyl, 2-naphthyl),N-hydroxytetrazolyl, N-hydroxytriazolyl, N-hydroxyimidazolyl,anthracenyl (1-anthracenyl, 2-anthracenyl, 3-anthracenyl), thiophenyl(2-thienyl, 3-thienyl), furyl (2-furyl, 3-furyl), indolyl, oxadiazolyl,isoxazolyl, quinazolinyl, fluorenyl, xanthenyl, isoindanyl, benzhydryl,acridinyl, thiazolyl, pyrrolyl (2-pyrrolyl), pyrazolyl (3-pyrazolyl),imidazolyl (1-imidazolyl, 2-imidazolyl, 4-imidazolyl, 5-imidazolyl),triazolyl (1,2,3-triazol-1-yl, 1,2,3-triazol-2-yl 1,2,3-triazol-4-yl,1,2,4-triazol-3-yl), oxazolyl (2-oxazolyl, 4-oxazolyl, 5-oxazolyl),thiazolyl (2-thiazolyl, 4-thiazolyl, 5-thiazolyl), pyridyl (2-pyridyl,3-pyridyl, 4-pyridyl), pyrimidinyl (2-pyrimidinyl, 4-pyrimidinyl,5-pyrimidinyl, 6-pyrimidinyl), pyrazinyl, pyridazinyl (3-pyridazinyl,4-pyridazinyl, 5-pyridazinyl), quinolyl (2-quinolyl, 3-quinolyl,4-quinolyl, 5-quinolyl, 6-quinolyl, 7-quinolyl, 8-quinolyl), isoquinolyl(1-isoquinolyl, 3-isoquinolyl, 4-isoquinolyl, 5-isoquinolyl,6-isoquinolyl, 7-isoquinolyl, 8-isoquinolyl), benzo[b]furanyl(2-benzo[b]furanyl, 3-benzo[b]furanyl, 4-benzo[b]furanyl,5-benzo[b]furanyl, 6-benzo[b]furanyl, 7-benzo[b]furanyl),2,3-dihydro-benzo[b]furanyl (2-(2,3-dihydro-benzo[b]furanyl),3-(2,3-dihydro-benzo[b]furanyl), 4-(2,3-dihydro-benzo[b]furanyl),5-(2,3-dihydro-benzo[b]furanyl), 6-(2,3-dihydro-benzo[b]furanyl),7-(2,3-dihydro-benzo[b]furanyl), benzo[b]thiophenyl(2-benzo[b]thiophenyl, 3-benzo[b]thiophenyl, 4-benzo[b]thiophenyl,5-benzo[b]thiophenyl, 6-benzo[b]thiophenyl, 7-benzo[b]thiophenyl),2,3-dihydro-benzo[b]thiophenyl, (2-(2,3-dihydro-benzo[b]thiophenyl),3-(2,3-dihydro-benzo[b]thiophenyl), 4-(2,3-dihydro-benzo[b]thiophenyl),5-(2,3-dihydro-benzo[b]thiophenyl), 6-(2,3-dihydro-benzo[b]thiophenyl),7-(2,3-dihydro-benzo[b]thiophenyl), indolyl (1-indolyl, 2-indolyl,3-indolyl, 4-indolyl, 5-indolyl, 6-indolyl, 7-indolyl), indazole(1-indazolyl, 3-indazolyl, 4-indazolyl, 5-indazolyl, 6-indazolyl,7-indazolyl), benzimidazolyl (1-benzimidazolyl, 2-benzimidazolyl,4-benzimidazolyl, 5-benzimidazolyl, 6-benzimidazolyl, 7-benzimidazolyl,8-benzimidazolyl), benzoxazolyl (1-benzoxazolyl, 2-benzoxazolyl),benzothiazolyl (1-benzothiazolyl, 2-benzothiazolyl, 4-benzothiazolyl,5-benzothiazolyl, 6-benzothiazolyl, 7-benzothiazolyl), carbazolyl(1-carbazolyl, 2-carbazolyl, 3-carbazolyl, 4-carbazolyl),5H-dibenz[b,f]azepine (5H-dibenz[b,f]azepin-1-yl,5H-dibenz[b,f]azepine-2-yl, 5H-dibenz[b,f]azepine-3-yl,5H-dibenz[b,f]azepine-4-yl, 5H-dibenz[b,f]azepine-5-yl),10,11-dihydro-5H-dibenz[b,f]azepine(10,11-dihydro-5H-dibenz[b,f]azepine-1-yl,10,11-dihydro-5H-dibenz[b,f]azepine-2-yl,10,11-dihydro-5H-dibenz[b,f]azepine-3-yl,10,11-dihydro-5H-dibenz[b,f]azepine-4-yl,10,11-dihydro-5H-dibenz[b,f]azepine-5-yl), and the like.

Heterocyclylalkyl groups are cyclic alkyl groups as defined above inwhich a hydrogen or carbon bond of an alkyl group is replaced with abond to a heterocyclyl group as defined above. Representativeheterocyclyl alkyl groups include, but are not limited to, furan-2-ylmethyl, furan-3-yl methyl, pyridine-2-yl methyl (α-picolyl),pyridine-3-yl methyl (β-picolyl), pyridine-4-yl methyl (γ-picolyl),tetrahydrofuran-2-yl ethyl, and indol-2-yl propyl. Heterocyclylalkylgroups can be substituted on the heterocyclyl moiety, the alkyl moiety,or both.

Heteroarylalkyl groups are alkyl groups as defined above in which ahydrogen or carbon bond of an alkyl group is replaced with a bond to aheteroaryl group as defined above. Heteroarylalkyl groups can besubstituted on the heteroaryl moiety, the alkyl moiety, or both.

By a “ring system” or “ring,” as the term is used herein, is meant amoiety comprising one, two, three or more rings, which can besubstituted with non-ring groups or with other ring systems, or both,which can be fully saturated, partially unsaturated, fully unsaturated,or aromatic, and when the ring system includes more than a single ring,the rings can be fused, bridging, or spirocyclic. By “spirocyclic” ismeant the class of structures wherein two rings are fused at a singletetrahedral carbon atom, as is well known in the art.

A “monocyclic, bicyclic or polycyclic, aromatic or partially aromaticring” as the term is used herein refers to a ring system including anunsaturated ring possessing 4n+2 μl electrons, or a partially reduced(hydrogenated) form thereof. The aromatic or partially aromatic ring caninclude additional fused, bridged, or spiro rings that are notthemselves aromatic or partially aromatic. For example, naphthalene andtetrahydronaphthalene are both a “monocyclic, bicyclic or polycyclic,aromatic or partially aromatic ring” within the meaning herein. Also,for example, a benzo-[2.2.2]-bicyclooctane is also a “monocyclic,bicyclic or polycyclic, aromatic or partially aromatic ring” within themeaning herein, containing a phenyl ring fused to a bridged bicyclicsystem. A fully saturated ring has no double bonds therein, and iscarbocyclic or heterocyclic depending on the presence of heteroatomswithin the meaning herein.

The term “alkoxy” refers to an oxygen atom connected to an alkyl group,including a cycloalkyl group, as are defined above. Examples of linearalkoxy groups include but are not limited to methoxy, ethoxy, n-propoxy,n-butoxy, n-pentyloxy, n-hexyloxy, and the like. Examples of branchedalkoxy include but are not limited to isopropoxy, sec-butoxy,tert-butoxy, isopentyloxy, isohexyloxy, and the like. Examples of cyclicalkoxy include but are not limited to cyclopropyloxy, cyclobutyloxy,cyclopentyloxy, cyclohexyloxy, and the like.

The terms “aryloxy” and “arylalkoxy” refer to, respectively, an arylgroup bonded to an oxygen atom and an aralkyl group bonded to the oxygenatom at the alkyl moiety. Examples include but are not limited tophenoxy, naphthyloxy, and benzyloxy.

An “acyl” group as the term is used herein refers to a group containinga carbonyl moiety wherein the group is bonded via the carbonyl carbonatom. The carbonyl carbon atom is also bonded to another carbon atom,which can be part of an alkyl, aryl, aralkyl cycloalkyl,cycloalkylalkyl, heterocyclyl, heterocyclylalkyl, heteroaryl,heteroarylalkyl group or the like. In the special case wherein thecarbonyl carbon atom is bonded to a hydrogen, the group is a “formyl”group, an acyl group as the term is defined herein. An acyl group caninclude 0 to about 12-20 additional carbon atoms bonded to the carbonylgroup. An acyl group can include double or triple bonds within themeaning herein. An acryloyl group is an example of an acyl group. Anacyl group can also include heteroatoms within the meaning here. Anicotinoyl group (pyridyl-3-carbonyl) group is an example of an acylgroup within the meaning herein. Other examples include acetyl, benzoyl,phenylacetyl, pyridylacetyl, cinnamoyl, and acryloyl groups and thelike. When the group containing the carbon atom that is bonded to thecarbonyl carbon atom contains a halogen, the group is termed a“haloacyl” group. An example is a trifluoroacetyl group.

The term “amine” or “amino” includes primary, secondary, and tertiaryamines having, e.g., the formula N(group)₃ wherein each group canindependently be H or non-H, such as alkyl, aryl, and the like. Aminesinclude but are not limited to R—NH₂, for example, alkylamines,arylamines, alkylarylamines; R₄NH wherein each R is independentlyselected, such as dialkylamines, diarylamines, aralkylamines,heterocyclylamines and the like; and R₅N wherein each R is independentlyselected, such as trialkylamines, dialkylarylamines, alkyldiarylamines,triarylamines, and the like. The term “amine” also includes ammoniumions as used herein.

An “amino” group is a substituent of the form —NH₂, —NHR, —N(R)₂, —N(R)₃⁺, wherein each R is independently selected, and protonated forms ofeach. Accordingly, any compound substituted with an amino group can beviewed as an amine.

An “ammonium” ion includes the unsubstituted ammonium ion NH₄, butunless otherwise specified, it also includes any protonated orquaternarized forms of amines. Thus, trimethylammonium hydrochloride andtetramethylammonium chloride are both ammonium ions, and amines, withinthe meaning herein.

The term “amide” (or “amido”) includes C- and N-amide groups, i.e.,—C(O)N(R)₂, and —NRC(O)R— groups, respectively. Amide groups thereforeinclude but are not limited to carbamoyl groups (—C(O)NH₂) and formamidegroups (—NHC(O)H). A “carboxamido” group is a group of the formulaC(O)N(R)₂, wherein R can be H, alkyl, aryl, etc.

The term “urethane” (or “carbamyl”) includes N- and O-urethane groups,i.e., —NRC(O)OR and —OC(O)N(R)₂ groups, respectively.

The term “sulfonamide” (or “sulfonamido”) includes S- and N-sulfonamidegroups, i.e., —SO₂NR₂ and —NRSO₂R groups, respectively. Sulfonamidegroups therefore include but are not limited to sulfamoyl groups(—SO₂NH₂).

The term “amidine” or “amidino” includes groups of the formula—C(NR)N(R)₂. Typically, an amidino group is —C(NH)NH₂.

The term “guanidine” or “guanidino” includes groups of the formula—NRC(NR)N(R)₂. Typically, a guanidino group is —NHC(NH)NH₂.

“Halo,” “halogen,” and “halide” include fluorine, chlorine, bromine andiodine.

The terms “comprising,” “including,” “having,” “composed of,” areopen-ended terms as used herein, and do not preclude the existence ofadditional elements or components. In a claim element, use of the forms“comprising,” “including,” “having,” or “composed of” means thatwhatever element is comprised, had, included, or composes is notnecessarily the only element encompassed by the subject of the clausethat contains that word.

A “salt” as is well known in the art includes an organic compound suchas a carboxylic acid, a sulfonic acid, or an amine, in ionic form, incombination with a counterion. For example, acids in their anionic formcan form salts with cations such as metal cations, for example sodium,potassium, and the like; with ammonium salts such as NH₄ ⁺ or thecations of various amines, including tetraalkyl ammonium salts such astetramethylammonium, or other cations such as trimethylsulfonium, andthe like. A “pharmaceutically acceptable” or “pharmacologicallyacceptable” salt is a salt formed from an ion that has been approved forhuman consumption and is generally non-toxic, such as a chloride salt ora sodium salt. A “zwitterion” is an internal salt such as can be formedin a molecule that has at least two ionizable groups, one forming ananion and the other a cation, which serve to balance each other. Forexample, amino acids such as glycine can exist in a zwitterionic form. A“zwitterion” is a salt within the meaning herein. The compounds of thepresent invention may take the form of salts. The term “salts” embracesaddition salts of free acids or free bases which are compounds of theinvention. Salts can be “pharmaceutically-acceptable salts.” The term“pharmaceutically-acceptable salt” refers to salts which possesstoxicity profiles within a range that affords utility in pharmaceuticalapplications. Pharmaceutically unacceptable salts may nonethelesspossess properties such as high crystallinity, which have utility in thepractice of the present invention, such as for example utility inprocess of synthesis, purification or formulation of compounds of theinvention.

Suitable pharmaceutically-acceptable acid addition salts may be preparedfrom an inorganic acid or from an organic acid. Examples of inorganicacids include hydrochloric, hydrobromic, hydriodic, nitric, carbonic,sulfuric, and phosphoric acids. Appropriate organic acids may beselected from aliphatic, cycloaliphatic, aromatic, araliphatic,heterocyclic, carboxylic and sulfonic classes of organic acids, examplesof which include formic, acetic, propionic, succinic, glycolic,gluconic, lactic, malic, tartaric, citric, ascorbic, glucuronic, maleic,fumaric, pyruvic, aspartic, glutamic, benzoic, anthranilic,4-hydroxybenzoic, phenylacetic, mandelic, embonic (pamoic),methanesulfonic, ethanesulfonic, benzenesulfonic, pantothenic,trifluoromethanesulfonic, 2-hydroxyethanesulfonic, p-toluenesulfonic,sulfanilic, cyclohexylaminosulfonic, stearic, alginic, β-hydroxybutyric,salicylic, galactaric and galacturonic acid. Examples ofpharmaceutically unacceptable acid addition salts include, for example,perchlorates and tetrafluoroborates.

Suitable pharmaceutically acceptable base addition salts of compounds ofthe invention include, for example, metallic salts including alkalimetal, alkaline earth metal and transition metal salts such as, forexample, calcium, magnesium, potassium, sodium and zinc salts.Pharmaceutically acceptable base addition salts also include organicsalts made from basic amines such as, for example,N,N-dibenzylethylenediamine, chloroprocaine, choline, diethanolamine,ethylenediamine, meglumine (N-methylglucamine) and procaine. Examples ofpharmaceutically unacceptable base addition salts include lithium saltsand cyanate salts. Although pharmaceutically unacceptable salts are notgenerally useful as medicaments, such salts may be useful, for exampleas intermediates in the synthesis of Formula I compounds, for example intheir purification by recrystallization. All of these salts may beprepared by conventional means from the corresponding compound accordingto Formula I by reacting, for example, the appropriate acid or base withthe compound according to Formula I. The term “pharmaceuticallyacceptable salts” refers to nontoxic inorganic or organic acid and/orbase addition salts, see, for example. Lit et al., Salt Selection forBasic Drugs (1986), Int J. Pharm., 33, 201-217, incorporated byreference herein.

A “hydrate” is a compound that exists in a composition with watermolecules. The composition can include water in stoichiometricquantities, such as a monohydrate or a dihydrate, or can include waterin random amounts. As the term is used herein a “hydrate” refers to asolid form, i.e., a compound in water solution, while it may behydrated, is not a hydrate as the term is used herein.

A “solvate” is a similar composition except that a solvent other thatwater replaces the water. For example, methanol or ethanol can form an“alcoholate”, which can again be stoichiometric or non-stoichiometric.As the term is used herein a “solvate” refers to a solid form, i.e., acompound in solution in a solvent, while it may be solvated, is not asolvate as the term is used herein.

A “prodrug” as is well known in the art is a substance that can beadministered to a patient where the substance is converted in vivo bythe action of biochemicals within a mammal's body (e.g., in a patient'sbody), such as enzymes, to the active pharmaceutical ingredient.Examples of prodrugs include esters of carboxylic acid groups, which canbe hydrolyzed by endogenous esterases as are found in the bloodstream ofhumans and other mammals.

In addition, where features or aspects of the invention are described interms of Markush groups, those skilled in the art will recognize thatthe invention is also thereby described in terms of any individualmember or subgroup of members of the Markush group. For example, if X isdescribed as selected from the group consisting of bromine, chlorine,and iodine, claims for X being bromine and claims for X being bromineand chlorine are fully described. Moreover, where features or aspects ofthe invention are described in terms of Markush groups, those skilled inthe art will recognize that the invention is also thereby described interms of any combination of individual members or subgroups of membersof Markush groups. Thus, for example, if X is described as selected fromthe group consisting of bromine, chlorine, and iodine, and Y isdescribed as selected from the group consisting of methyl, ethyl, andpropyl, claims for X being bromine and Y being methyl are fullydescribed.

In various embodiments, the compound or set of compounds, either per seor as are used in practice of embodiments of the inventive methods, canbe any one of any of the combinations and/or sub-combinations of thevarious embodiments recited.

Provisos may apply to any of the disclosed categories or embodimentswherein any one or more of the other above disclosed embodiments orspecies may be excluded from such categories or embodiments.

Compounds

The compounds of the invention include any of those described herein,including compounds shown in the Examples. In some instances, thecompounds are embraced by formula I:

wherein:

-   -   A and B are separately each a heterocyclyl ring or a phenyl        group, where the A ring has x R₁ substituents;    -   C is phenyl or pyridinyl;    -   D is heterocyclyl ring;    -   linkage₁ is a single bond between A and B;    -   linkage₂ is a C₁-C₃ alkylamido, amidoalkyl, amino, urea,        alkylurea, or ureaalkyl with a first and second terminal atom;    -   y is an integer of 0-3, and when y is 0, the linkage between the        rings is a single bond;    -   x is an integer of 0-4;    -   v is an integer of 0-2;    -   R₁ substituents on the A ring are selected from amino,        optionally substituted C₁-C₄ alkyl, optionally substituted        ether, optionally substituted C₁-C₄ alkoxy, oxy, hydroxy,        —NH—SO₂-phenyl-(R₅), and cyano;    -   R₂ substituents on the B ring are selected from amino, and        optionally substituted C₁-C₄ alkyl;    -   R₃ substituents on the C ring are selected from halo, CF₃,        optionally substituted C₁-C₄ alkyl, and optionally substituted        heteroaryl; and    -   R₄ substituents on the D ring are selected from optionally        substituted C₁-C₄ alkyl, optionally substituted C₁-C₄ alkoxy,        (optionally substituted C₁-C₄ alkylene)-OH, hydroxy, optionally        substituted aryl, optionally substituted benzyl, and optionally        substituted benzaldehyde;    -   R₅ is halo; or    -   a pharmaceutically acceptable salt thereof.

In some cases, the A ring is heterocyclyl ring. In some cases, the Aring is a heterocyclyl that is a single non-fused ring. In other cases,the A ring is a heterocyclyl that is a fusion of two or three rings. Inother cases, the A ring is a heterocyclyl that is a fusion of two rings.In some cases, the A ring of the compounds described herein isheteroaromatic. In some embodiments, the A ring is a single non-fused5-membered heteroaryl. In some embodiments, the A ring is a singlenon-fused 6-membered heteroaryl. In some embodiments, the A ring ispyridinyl, pyridazinyl, pyrimidinyl, or pyrazinyl. In some embodiments,the A ring is pyridinyl. In some cases, the A ring is a heteroaryl thatis a fusion of two rings. Examples of A rings include indazole,imadazopyridine, imadazopyrazine, imadazopyridazine, pyrrolopyridine,hexahydrothienopyrimidine, imidazole, pyrazole, pyrazine, pyridine,pyrimidine, phenylpyrimidinamine, quinolinyl, isoquinolinyl,tetrahydroquinolinyl, and quinazolinyl. In some embodiments, the A ringis isoquinolinyl. In some embodiments, the A ring is quinazolinyl. Forexample, the A ring can be selected from any of the following:

In some instances, the A ring is

In some instances, the A ring is

In some instances, the A ring is

In some embodiments, the R₁ substituents on the A ring are selected fromamino, optionally substituted C₁-C₄ alkyl, and hydroxy. In someembodiments, the R₁ substituents on the A ring can, for example, beselected from amino and optionally substituted C₁-C₃ alkyl. In somecases, the R₁ substituents on the A ring are selected from —NH₂ and—CH₃. In addition, in some cases x=0, but in other cases x=1. In somecases, x=2. In some cases, x=3. For example, x can in some cases be 0,1, or 2 when the A ring is a fusion of two rings. In other cases, x=1 or2 when the A ring is a single, nonfused ring.

The B ring can be a single, non-fused ring. In some embodiments, the Bring is single, non-fused 5-membered ring. In some embodiments, the Bring is pyrazolyl, imidazolyl, or triazolyl. In some cases, the B ringis pyrazolyl. Alternatively, the B ring can be a fusion of two rings. Insome embodiments, the B ring is indazolyl or benzoxazolyl. For example,the B ring can be selected from any of the following:

In some cases, the B ring is

In some cases, the B ring is

In some cases, the B ring is

In some embodiments, R₂ substituents on the B ring are optionallysubstituted C₁-C₄ alkyl. In some embodiments, R₂ substituents on the Bring are —CH₃.

In some cases the C ring can be a phenyl group, and in other cases, apyridinyl group. In some instances, the C ring is phenyl. In someembodiments, the R₃ substituents on the C ring are selected from halo,CF₃, optionally substituted C₁-C₄ alkyl, and optionally substitutedheteroaryl. In some embodiments, the R₃ substituent is halo. In someembodiments, the R₃ substituent is CF₃. In some embodiments, the R₃substituent is optionally substituted C₁-C₄ alkyl. In some embodiments,the R₃ substituent is optionally substituted heteroaryl.

The linkage₂ group can, for example, be selected from any of thefollowing:

wherein a hydrogen atom on Ring B is replaced by the first terminal atomof linkage₂ and a hydrogen atom on Ring C is replaced by the secondterminal atom of linkage₂. In some cases, linkage₂ is

In some cases, linkage₂ is

In some embodiments, D ring is a heterocyclyl ring containing at leastone N atom. In some embodiments, the D ring is piperidinyl, piperazinyl,or morpholinyl. The D ring can, for example, be selected from any of thefollowing:

In some embodiments, Ring D is

In some embodiments, the R₄ substituents on the D ring are optionallysubstituted C₁-C₄ alkyl. The R₄ substituents on the D ring can in somecases be selected from CH₃. CH₃CHCH₃. CH₃CH(CH₂)CH₃, and CH₃CH₂CH₃OH. Insome cases, R₄ is CH₃. In some embodiments, R₄ is optionally substitutedC₁-C₄ alkoxy. In some embodiments, R₄ is (optionally substituted C₁-C₄alkylene)-OH. In some embodiments, R₄ is (optionally substituted C₁alkylene)-OH. In some embodiments, R₄ is (optionally substituted C₂alkylene)-OH. In some embodiments, R₄ is (optionally substituted C₃alkylene)-OH. In some embodiments, R is (optionally substituted C₄alkylene)-OH. In some embodiments, R₄ is hydroxyl. In some embodiments,R₄ is optionally substituted aryl. In some embodiments, R₄ is phenyl. Insome embodiments, R₄ is optionally substituted benzyl. In someembodiments, v is 1. In some embodiments, v is 2. In some embodiments, yis 1. In some embodiments, y is 2. In some embodiments, y is 3.

In some instances, the compounds are embraced by formula Ia:

wherein,

-   -   A₁ is N, CH, or CR₁; A₂ is N, CH, or CR₁; A₃ is N. CH, or CR₁;        A₄ is N, CH, or CR₁; A₅ is N, CH, or CR₁; A₆ is N, CH, or CR₁;        A₇ is N CH, or CR₁;    -   v is an integer of 0-2;    -   Each R₁ is NH₂ or OH; provided that the number of R₁ on the A        ring does not exceed 4;    -   B is selected from:

-   -   each R₂ is independently selected from H and optionally        substituted C₁-C₄ alkyl;    -   X₁ and X₂ are each independently CH₂ or NH; with the provision        that X₁ and X₂ are not each CH₂;    -   R₃ is selected from H, halo, CF₃, optionally substituted C₁-C₄        alkyl, and optionally substituted heteroaryl;    -   D is heterocyclyl ring containing at least one N atom;    -   each R₄ is selected from H, optionally substituted C₁-C₄ alkyl,        optionally substituted C₁-C₄ alkoxy, (optionally substituted        C₁-C₄ alkylene)-OH, hydroxy, optionally substituted aryl, and        optionally substituted benzyl; or    -   a pharmaceutically acceptable salt thereof.

In some embodiments, A₁ is CH or CR₁; A₂ is N; A₃ is CH or CR₁; A₄ is N,CH, or CR₁; As is CH or CR₁; A₆ is CH or CR₁; and A₇ is CH or CR₁. Insome embodiments, A₁ is CH or CR₁; A₂ is N; A₃ is CH or CR₁; A₄ is N; A₅is CH or CR₁; A₆ is CH or CR₁; and A₇ is CH or CR₁. In some embodiments.A₁ is CH or CR₁; A₂ is N; A₃ is CH or CR₁; A₄ is CH or CR₁; A₅ is CH orCR₁; A₆ is CH or CR₁; and A₇ is CH or CR₁. In some embodiments, A, isCH; A₂ is N; A₃ is CR₁; A₄ is N; A₅ is CH; A₆ is CH; and A₇ is CH. Insome embodiments, A₁ is CH; A₂ is N; A₃ is CR₁; A₄ is CR₁; A₅ is CH; A₆is CH; and A₇ is CH.

In some embodiments, A₁ is CH or CR₁; A₂ is N; A₃ is CH or CR₁; A₄ is N;A₅ is CH; A₆ is CH; and A₇ is CH. In some embodiments, A₁ is CH or CR₁;A₂ is N; A₃ is CH or CR₁; A₄ is CH or CR₁; A₅ is CH; A₆ is CH; and A₇ isCH.

In some embodiments, A₁ is N. In some embodiments, A₁ is CH. In someembodiments, A₁ is CR₁, and R₁ is OH. In some embodiments, A₁ is CR₁,and R₁ is NH₂. In some embodiments, A₂ is N. In some embodiments, A₂ isCH. In some embodiments, A₂ is CR₁, and R₁ is OH. In some embodiments,A₂ is CR₁, and R₁ is NH₂. In some embodiments, A₃ is N. In someembodiments, A₃ is CH. In some embodiments, A₃ is CR₁, and R₁ is OH. Insome embodiments, A₃ is CR₁, and R₁ is NH₂. In some embodiments, A₄ isN. In some embodiments, A₄ is CH. In some embodiments, A₄ is CR₁, and R₁is OH. In some embodiments, A₄ is CR₁, and R₁ is NH₂. In someembodiments, A₅ is N. In some embodiments, A₅ is CH. In someembodiments, A₅ is CR₁, and R₁ is OH. In some embodiments, A₅ is CR₁,and R₁ is NH₂. In some embodiments, A₆ is N. In some embodiments, A₆ isCH. In some embodiments, A₆ is CR₁, and R₁ is OH. In some embodiments,A₆ is CR₁, and R₁ is NH₂. In some embodiments, A₇ is N. In someembodiments, A₇ is CH. In some embodiments, A₇ is CR₁, and R₁ is OH. Insome embodiments. A₇ is CR₁, and R₁ is NH₂.

In some embodiments, B is

In some embodiments, B is

In some embodiments, B is

In some embodiments, each R₂ is H. In some embodiments, each R₂ isoptionally substituted C₁-C₄ alkyl. In some embodiments, each R₂ ismethyl.

In some embodiments, X₁ and X₂ are each NH. In some embodiments, X₁ isCH₂ and X₂ is NH. In some embodiments, X₁ is NH and X₂ is CH₂. In someembodiments, R₃ is H. In some embodiments, R₃ is halo. In someembodiments, R₃ is CF₃. In some embodiments, R₃ is optionallysubstituted C₁-C₄ alkyl. In some embodiments, R₃ is optionallysubstituted heteroaryl.

In some embodiments, D is selected from:

In some embodiments, D is

In some embodiments, D is

In some embodiments, D is

In some embodiments, D is

In some embodiments, D is

In some embodiments, v is 0. In some embodiments, v is 1. In someembodiments, R₄ is H. In some embodiments, R₄ is optionally substitutedC₁-C₄ alkyl. In some embodiments, R₄ is Me, Et, or i-Pr. In someembodiments, R₄ is optionally substituted C₁-C₄ alkylene)-OH. In someembodiments, R₄ is optionally substituted C₁alkylene)-OH. In someembodiments, R₄ is optionally substituted C₂alkylene)-OH. In someembodiments, R₄ is optionally substituted C₃ alkylene)-OH. In someembodiments, R₄ is optionally substituted C₄ alkylene)-OH. In someembodiments, R₄ is hydroxyl. In some embodiments, R₄ is optionallysubstituted aryl. In some embodiments, R₄ is phenyl. In someembodiments, R₄ is optionally substituted benzyl. In some embodiments, vis 2. In some embodiments, at least one R₄ is H. In some embodiments, atleast one R₄ is optionally substituted C₁-C₄ alkyl. In some embodiments,at least one R₄ is Me, Et, or i-Pr. In some embodiments, at least one R₄is optionally substituted C₁-C₄ alkylene)-OH. In some embodiments, atleast one R₄ is hydroxyl. In some embodiments, at least one R₄ isoptionally substituted aryl. In some embodiments, at least one R₄ isoptionally substituted benzyl.

In some instances, the compounds are embraced by formula Ib:

In some instances, the compounds are embraced by formula Ic:

In some instances, the compounds are embraced by formula Id:

In some instances, the compounds are embraced by formula Ie:

In some instances, the compounds are the compounds as shown in Tables 1,2, 3, and 4.

TABLE 1 Compound No. Structure Name 1

1-(1-methyl-6-(pyridin-3-yl)-1H- indazol-3-yl)-3-(4-((4-methylpiperazin-1-yl)methyl)-3- (trifluoromethyl)phenyl)urea 2

1-(5-(benzo[d]isoxazol-6-yl)-1- methyl-1H-pyrazol-3-yl)-3-(4-((4-methylpiperazin-1-yl)methyl)-3- (trifluoromethyl)phenyl)urea 3

1-(5-(benzo[d]isoxazol-5-yl)-1- methyl-1H-pyrazol-3-yl)-3-(4-((4-methylpiperazin-1-yl)methyl)-3- (trifluoromethyl)phenyl)urea 4

1-(5-(imidazo[1,2-a]pyridin-7-yl)- 1-methyl-1H-pyrazol-3-yl)-3-(4-((4-methylpiperazin-1-yl)methyl)- 3-(trifluoromethyl)phenyl)urea 5

1-(5-(imidazo[1,2-a]pyridin-8-yl)- 1-methyl-1H-pyrazol-3-yl)-3-(4-((4-methylpiperazin-1-yl)methyl)- 3-(trifluoromethyl)pheny)urea 6

1-(1-methyl-5-(quinoxalin-5-yl)- 1H-pyrazol-3-yl)-3-(4-((4-methylpiperazin-1-yl)methyl)-3- (trifluoromethyl)phenyl)urea 7

1-(4-((4-methylpiperazin-1- yl)methyl)-3- (trifluoromethyl)phenyl)-3-(5-(pyridin-3-yl)-1H-pyrazol-3- yl)urea 8

1-(5-(2-(difluoromethyl)-4-oxo- 3,4-dihydroquinazolin-6-yl)-1-methyl-1H-pyrazol-3-yl)-3-(4-((4- methylpiperazin-1-yl)methyl)-3-(trifluoromethyl)phenyl)urea 9

1-(6-(2-aminopyrimidin-5-yl)-1- methyl-1H-indazol-3-yl)-3-(4-((4-methylpiperazin-1-yl)methyl)-3- (trifluoromethyl)phenyl)urea 10

1-6-(5-aminopyrazin-2-yl)-1- methyl-1H-indazol-3-yl)-3-(4-((4-methylpiperazin-1-yl)methyl)-3- (trifluoromethyl)phenyl)urea 11

1-(6-(2-aminopyrimidin-5-yl)-1H- indazol-3-yl)-3-(4-(4-methylpiperazin-1-yl)methyl)-3- (trifluoromethyl)phenyl)urea 12

1-(1-methyl-5-(1-methyl-1H- pyrrolo[2,3-b]pyridin-4-yl)-1H-pyrazol-3-yl)-3-(4-((4- methylpiperazin-1-yl)methyl)-3-(trifluoromethyl)phenyl)urea 13

1-(4-(piperazin-1-ylmethyl)-3- (trifluoromethyl)phenyl)-3-(2-(pyridin-3-yl)benzo[d]oxazol-5- yl)urea 14

1-(4-((4-benzylpiperazin-1- yl)methyl)-3- (trilfuoromethyl)phenyl)-3-(2-(pyridin-3-yl)benzo[d]oxazol-5- yl)urea 15

1-(4-((4-methylpiperazin-1- yl)methyl)-3- (trifluoromethyl)phenyl)-3-(2-(pyridin-3-yl)benzo[d]oxazol-5- yl)urea 16

1-(4-((4-methylpiperazin-1- yl)methyl)-3- (trifluoromethyl)phenyl)-3-(2-(pyrazolo[1,5-a]pyridin-3- yl)benzo[d]oxazol-5-yl)urea 17

1-(6-methyl-2-(pyrazolo[1,5- a]pyridin-3-yl)benzo[d]oxazol-5-yl)-3-(4-((4-methylpiperazin-1- yl)methyl)-3-(trifluoromethyl)phenyl)urea 18

1-(4-methyl-2-(pyrazolo[1,5- a]pyridin-3-yl)benzo[d]oxazol-5-yl)-3-(4-((4-methylpiperazin-1- yl)methyl)-3-(trifluoromethyl)phenyl)urea 19

1-(5-(isoquinolin-7-yl)-1-methyl- 1H-pyrazol-3-yl)-3-(3-(2-(4-methylpiperazin-1- yl)ethyl)phenyl)urea 20

N-(5-(isoquinolin-7-yl)-1-methyl- 1H-pyrazol-3-yl)-3-(1H-pyrazol-1-yl)benzamide 21

1-(5-(isoquinolin-7-yl)-1-methyl- 1H-pyrazol-3-yl)-3-(2-(1-methyl-1H-pyrazol-4-yl)-4-((4- methylpiperazin-1- yl)methyl)phenyl)urea

TABLE 2 Compound No. Structure Name 22

1-(1-methyl-5-(quinazolin-6-yl)- 1H-pyrazol-3-yl)-3-(4-((4-methylpiperazin-1-yl)methyl)-3- (trifluoromethyl)phenyl)urea 23

1-(5-(2-hydroxyquinolin-7-yl)-1- methyl-1H-pyrazol-3-yl)-3-(4-((4-methylpiperazin-1-yl)methyl)-3- (trithoromethyl)phenyl)urea 24

1-(5-(isoquinolin-7-yl)-1-methyl- 1H-pyrazol-3-yl)-3-(4-((4-methylpiperazin-1-yl)methyl)-3- (trifluoromethyl)phenyl)urea 25

1-(1-methyl-5-(quinolin-3-yl)-1H- pyrazol-3-yl)-3-(4-((4-methylpiperazin-1-yl)methyl)-3- (trifluoromethyl)phenyl)urea 26

1-(5-(3-aminoisoquinolin-7-yl)-1- methyl-1H-pyrazol-3-yl)-3-(4-((4-methylpiperazin-1-yl)methyl)-3- (trifluoromethyl)phenyl)urea 27

1-(5-(2-amino-4- hydroxyquinazolin-6-yl)-1-methyl-1H-pyrazol-3-yl)-3-(4-((4- methylpiperazin-1-yl)methyl)-3-(trifluoromethyl)phenyl)urea 28

1-(5-(4-aminoquinazolin-6-yl)-1- methyl-1H-pyrazol-3-yl)-3-(4-((4-methylpiperazin-1-yl)methyl)-3- (trifluoromethyl)phenyl)urea 29

1-(5-(2,4-diaminoquinazolin-6- yl)-1-methyl-1H-pyrazol-3-yl)-3-(4-((4-methylpiperazin-1- yl)methyl)-3- (trifluoromethyl)phenyl)urea 30

1-(5-(2-aminoquinazolin-6-yl)-1- methyl-1H-pyrazol-3-yl)-3-(4-((4-methylpiperazin-1-yl)methyl)-3- (trifluoromethyl)phenyl)urea 31

2-(5-(isoquinolin-7-yl)-1-methyl- 1H-pyrazol-3-yl)-N-(4-((4-methylpiperazin-1-yl)methyl)-3- (trifluoromethyl)phenyl)acetamide 32

2-(5-(3-aminoisoquinolin-7-yl)-1- methyl-1H-pyrazol-3-yl)-N-(4-((4-methylpiperazin-1-yl)methyl)- 3- (trifluoromethyl)phenyl)acetamide33

2-(5-(2-aminoquinazolin-6-yl)-1- methyl-1H-pyrazol-3-yl)-N-(4-((4-methylpiperazin-1-yl)methyl)- 3- (trifluoromethyl)phenyl)acetamide34

1-(5-(isoquinolin-7-yl)-1-methyl- 1H-1,2,4-triazol-3-yl)-3-(4-((4-methylpiperazin-1-yl)methyl)-3- (trifluoromethyl)phenyl)urea 35

1-(4-((4-ethylpiperizin-1- yl)methyl)-3- (trifluoromethyl)phenyl)-3-(5-(isoquinolin-7-yl)-1-methyl-1H- pyrazol-3-yl)urea 36

1-(4-((4-(2- hydroxyethyl)piperazin-1- yl)methyl)-3-(trifluoromethyl)phenyl)-3-(5- (isoquinolin-7-yl)-1-methyl-1H-pyrazol-3-yl)urea 37

1-(4-((4-isopropylpiperazin-1- yl)methyl)-3-(trifluoromethyl)phenyl)-3-(5- (isoquinolin-7-yl)-1-methyl-1H-pyrazol-3-yl)urea 38

1-(4-(azepan-1-ylmethyl)-3- (trifluoromethyl)phenyl)-3-(5-(isoquinolin-7-yl)-1-methyl-1H- pyrazol-3-yl)urea 39

1-(5-(isoquinolin-7-yl)-1-methyl- 1H-pyrazol-3-yl)-3-(4-(morpholinomethyl)-3- (trifluoromethyl)phenyl)urea 40

1-(5-(isoquinolin-7-yl)-1-methyl- 1H-pyrazol-3-yl)-3-(4-((4-phenylpiperidin-1-yl)methyl)-3- (trifluoromethyl)phenyl)urea 41

1-(4-((4-hydroxypiperidin-1- yl)methyl)-3-(trifluoromethyl)phenyl)-3-(5- (isoquinolin-7-yl)-1-methyl-1H-pyrazol-3-yl)urea 42

1-(5-(isoquinolin-7-yl)-1-methyl- 1H-pyrazol-3-yl)-3-(4-(piperidin-1-ylmethyl)-3- (trifluoromethyl)phenyl)urea 43

1-(5-(isoquinolin-7-yl)-1-methyl- 1H-pyrazol-3-yl)-3-(4-((2-methylpiperidin-1-yl)methyl)-3- (trifluoromethyl)phenyl)urea 44

1-(3-bromo-4-((4- methylpiperazin-1- yl)methyl)phenyl)-3-(5-(isoquinolin-7-yl)-1-methyl-1H- pyrazol-3-yl)urea 45

1-(5-(2-aminoquinazolin-6-yl)-1- methyl-1H-1,2,4-triazol-3-yl)-3-4-((4-methylpiperazin-1- yl)methyl)-3- (trifluoromethyl)phenyl)urea 46

1-(5-(isoquinolin-7-yl)-4-methyl- 4H-imidazol-2-yl)-3-(4-((4-methylpiperazin-1-yl)methyl)-3- (trifluoromethyl)phenyl)urea 47

1-(5-(isoquinolin-7-yl)-1-methyl- 1H-pyrazol-3-yl)-3-(4-((4-methylpiperazin-1- yl)methyl)phenyl)urea 48

1-(5-(3-aminoisoquinolin-7-yl)-1- methyl-1H-pyrazol-3-yl)-3-(4-((1-methylpiperidin-4-yl)methyl)-3- (trifluoromethyl)phenyl)urea 49

2-(5-(2-aminoquinazolin-6-yl)-1- methyl-1H-pyrazol-3-yl)-N-(4-((1-methylpiperidin-4-yl)methyl)- 3- (trifluoromethyl)phenyl)acetamide50

1-(5-(3-aminoisoquinolin-7-yl)- 1,4-dimethyl-1H-imidazol-2-yl)-3-(4-((4-methylpiperazin-1- yl)methyl)-3- (trifluoromethyl)phenyl)urea51

N-(5-(3-aminoisoquinolin-7-yl)-1- methyl-1H-pyrazol-3-yl)-2-(4-((4-methylpiperazin-1-yl)methyl)-3- (trifluoromethyl)phenyl)acetamide 52

1-(5-(3-aminoisoquinolin-7-yl)- 1H-pyrazol-3-yl)-3-(4-((4-methylpiperazin-1-yl)methyl)-3- (trifluoromethyl)phenyl)urea

TABLE 3 Compound No. Structure Name 53

1-(1-methyl-5-(4-(quinoxalin-5- yl)phenyl)-1H-pyrazol-3-yl)-3-(4-((4-methylpiperazin-1-yl)methyl)- 3-(trifluoromethyl)phenyl)urea 54

1-(5-(4-(imidazo[1,2-a]pyridin-8- yl)phenyl)-1-methyl-1H-pyrazol-3-yl)-3-(4-((4-methylpiperazin-1- yl)methyl)-3-(trifluoromethyl)phenyl)urea 55

1-(5-(4-(6-aminopyridin-3- yl)phenyl)-1H-pyrazol-3-yl)-3-(4-((4-methylpiperazin-1-yl)methyl)- 3-(trifluoromethyl)phenyl)urea 56

1-phenyl-3-(2-(pyridin-3- yl)benzo[d]oxazol-5-yl)urea 57

1-(2-(pyridin-3- yl)benzo[d]oxazol-5-yl)-3-(3-(trifluoromethyl)phenyl)urea 58

3-phenyl-N-(2-(pyridin-3- yl)benzo[d]oxazol-5- yl)propiolamide 59

(1S,2R)-2-phenyl-N-(2-(pyridin- 3-yl)benzo[d]oxazol-5-yl)cyclopropane-1-carboxamide 60

(Z)-3-phenyl-N-(2-(pyridin-3- yl)benzo[d]oxazol-5- yl)acrylamide 61

N-(5-(3-aminoisoquinolin-7-yl)-1- methyl-1H-pyrazol-3-yl)-4-((4-methylpiperazin-1-yl)methyl)-1- naphthamide 62

1-(5-(isoquinolin-7-yl)-1-methyl- 1H-pyrazol-3-yl)-3-(3-methyl-3,4-dihydro-2H-benzo[e][1,3]oxazin- 7-yl)urea 63

1-benzyl.-3-(5-(isoquinolin-7-yl)- 1-methyl-1H-pyrazol-3-yl)urea 64

1-(5-(isoquinolin-7-yl)-1-methyl- 1H-pyrazol-3-yl)-3-phenylurea 65

1-(5-(isoquinolin-7-yl)-1-methyl- 1H-pyrazol-3-yl)-3-(2-methoxyphenyl)urea 66

N-(5-(3-aminoisoquinolin-7-yl)-1- methyl-1H-pyrazol-3-yl)benzenesulfonamide 67

N-(5-(3-aminoisoquinolin-7-yl)-1- methyl-1H-pyrazol-3- yl)benzamide 68

1-(5-(isoquinolin-7-yl)-1-methyl- 1H-pyrazol-3-yl)-3-(2-(methylthio)phenyl)urea 69

1-(2-fluorophenyl)-3-(5- (isoquinolin-7-yl)-1-methyl-1H-pyrazol-3-yl)urea 70

4-(3-(5-(isoquinolin-7-yl)-1- methyl-1H-pyrazol-3-yl)ureido)-N-methylbenzenesulfonamide 71

1-(5-(3-aminoisoquinolin-7-yl)-1- methyl-1H-pyrazol-3-yl)-3-(4-((1-methylpiperidin-4- ylidene)methyl)-3- (trifluoromethyl)phenyl)urea 72

N-(5-(isoquinolin-7-yl)-1-methyl- 1H-pyrazol-3-yl)-3-(trithoromethyl)benzenesulfonamide 73

3-((5-(isoquinolin-7-yl)-1-methyl- 1H-pyrazol-3-yl)amino)-4-((4-((4-methylpiperazin-1-yl)methyl)-3- (trifluoromethyl)phenyl)amino)cyclobut-3-ene-1,2-dione 74

3-((5-(isoquinolin-7-yl)-1-methyl- 1H-pyrazol-3-yl)amino)-4-((4-((4-methylpiperazin-1- yl)methyl)phenyl)amino)cyclobut- 3-ene-1,2-dione 75

3-((5-(2-aminoquinazolin-6-yl)-1- methyl-1H-pyrazol-3-yl)amino)-4-((4-((4-methylpiperazin-1- yl)methyl)-3- (trifluoromethyl)phenyl)amino)cyclobut-3-ene-1,2-dione 76

3-((5-(2-aminoquinazolin-6-yl)-1- methyl-1H-pyrazol-3-yl)amino)-4-(cyclopentylamino)cyclobut-3- ene-1,2-dione

TABLE 4 Compound No. Structure 77

78

79

80

81

82

83

84

85

86

87

88

89

90

91

92

93

94

95

96

97

98

99

More specifically, the inventive compound can be any of the specificexamples shown herein as exemplary compounds of the invention.

Methods of Use

XBP1 is believed to sustain dendritic cell immunosuppressive activitywithin the tumor microenvironment by directly upregulating enzymesinvolved in triglyceride biosynthesis (Cubillos-Ruiz et al., Cell161(7): 1527-38 (2015)). XBP1, also known as X-box binding protein 1, isa transcription factor that regulates the expression of genes involvedin the proper functioning of the immune system and in the cellularstress response. It is believed that IRE1α-mediated XBP1 activation isfueled by the induction of reactive oxygen species and subsequentformation of peroxidized lipids.

The most conserved arm of the endoplasmic reticulum (ER) stress responseis the dual enzyme, IRE1α. Activated during periods of ER stress, theIRE1α endoribonuclease domain excises a short nucleotide fragment fromXhp1 mRNA to generate the functional transcription factor, XBP1. Thispotent, multitasking protein promotes cell survival by upregulatingexpression of a broad range of critical genes involved in proteinfolding and quality control. XBP1 drives the pathogenesis of triplenegative breast cancer (TNBC) by promoting tumor cell survival andmetastatic capacity under hypoxic conditions. Silencing of XBP1 in TNBCleads to suppression of tumor initiation, progression, and recurrence.

Unexpectedly, the inventors have identified a second mechanism by whichXBP1 promotes tumor progression: by confounding the development ofprotective antitumor immunity in the ovarian cancer tumormicroenvironment. Without XBP1, tumor resident dendritic cells failed toaccumulate intracellular lipids, which normally disrupt effectiveantigen cross-presentation. This pathological lipid accumulation isfundamentally driven by reactive oxygen species-mediated lipidperoxidation, which directly destabilizes protein-folding chaperoneswithin the endoplasmic reticulum to induce a state of ER stress and XBP1activation. Additionally, it is believed that IRE1α-mediated XBP1signaling is also critical for myeloid cell production ofimmunosuppressive prostaglandins such as prostaglandin E2 (PGE2).

Novel small-molecule IRE1α inhibitors with the ability to induce twoparallel and mutually reinforcing anti-tumor mechanisms, namely thedirect inhibition of tumor growth and the simultaneous induction ofrobust anti-tumor immunity are highly desirable, as no effective,targeted therapies currently exist for either TNBC or ovarian cancer.The compositions and methods described herein are novel IRE1α kinaseinhibitors that exhibit immune-modulatory properties. No currentlyexisting compounds possess activity in the presence of human or mouseovarian cancer ascites, a critical requirement for IRE1α inhibitor usageclinically.

Novel direct and indirect small molecule IRE1α inhibitors can preventlipid accumulation in myeloid cells exposed to ovarian cancer-derivedascites supernatants. Furthermore, the identified direct IRE1αinhibitors have unique chemical structures compared to currentlyavailable compounds, and therefore can have unique binding mechanisms,inhibitory activity, and off-target effects. Additionally, the inventorshave demonstrated that these compounds block myeloid cellimmunosuppression mediated by tumor-associated factors. The inventionalso includes novel uses for vitamin E and hydralazine derivatives,which indirectly prevent IRE1α activation and thereby suppress cancercell-induced lipid accumulation in myeloid dendritic cells.

The IRE1α-XBP1 pathway is therefore involved in a variety ofpathological conditions, including neurodegenerative diseases,inflammation, metabolic disorders, liver dysfunction, brain ischemia,heart ischemia, autoimmune diseases, and cancer. Hence, modulation ofthis pathway provides therapeutic methods useful for treatment of suchdiseases. The identified small molecule compounds can, for example, beemployed as therapeutic compounds that enhance dendritic cell and T cellanti-tumor activity in mammals. For example, the compounds disclosedherein can be used to treat murine and human ovarian cancers.

Hence, a method is described herein that includes administering any ofthe compounds or the composition described herein. The mammal can be inneed of administration of the composition. For example, the mammal canhave cancer, a neurodegenerative disease, inflammation, a metabolicdisorder, liver dysfunction, brain ischemia, heart ischemia, or anautoimmune disease. In some cases, the mammal has triple negative breastcancer or ovarian cancer.

Compositions and Combination Treatments

The IRE1α inhibitor compounds, their pharmaceutically acceptable saltsor hydrolyzable esters of the present invention may be combined with apharmaceutically acceptable carrier to provide pharmaceuticalcompositions useful for treating the biological conditions or disordersnoted herein in mammalian species, and more preferably, in humans. Theparticular carrier employed in these pharmaceutical compositions mayvary depending upon the type of administration desired (e.g.intravenous, oral, topical, suppository, or parenteral).

In preparing the compositions in oral liquid dosage forms (e.g.suspensions, elixirs and solutions), typical pharmaceutical media, suchas water, glycols, oils, alcohols, flavoring agents, preservatives,coloring agents and the like can be employed. Similarly, when preparingoral solid dosage forms (e.g. powders, tablets and capsules), carrierssuch as starches, sugars, diluents, granulating agents, lubricants,binders, disintegrating agents and the like can be employed.

Another aspect of an embodiment of the invention provides compositionsof the compounds of the invention, alone or in combination with anotherIRE1α inhibitor or another type of therapeutic agent, or both. Forexample, the compositions and methods described herein can include oneor more agents such as vitamin E, an antioxidant, and/or hydralazine.Such agents can sequester lipid peroxidation byproducts, and can beeffective treatments for controlling ER stress responses and sustainedIRE1α/XBP1 signaling in tumor-associated dendritic cells exposed, forexample, to ovarian cancer-derived ascites.

As set forth herein, compounds of the invention include stereoisomers,tautomers, solvates, hydrates, salts including pharmaceuticallyacceptable salts, and mixtures thereof. Compositions containing acompound of the invention can be prepared by conventional techniques,e.g. as described in Remington: The Science and Practice of Pharmacy,19th Ed., 1995, incorporated by reference herein. The compositions canappear in conventional forms, for example capsules, tablets, aerosols,solutions, suspensions or topical applications.

Typical compositions include one or more compounds of the invention anda pharmaceutically acceptable excipient which can be a carrier or adiluent. For example, the active compound wall usually be mixed with aearner, or diluted by a carrier, or enclosed within a, carrier which canbe in the form of an ampoule, capsule, sachet, paper, or othercontainer. When the active compound is mixed with a carrier, or when thecarrier serves as a diluent, it can be solid, semi-solid, or liquidmaterial that acts as a vehicle, excipient, or medium for the activecompound. The active compound can be adsorbed on a granular solidcarrier, for example contained in a sachet. Some examples of suitablecarriers are water, salt solutions, alcohols, polyethylene glycols, polyhydroxy ethoxy fated castor oil, peanut oil, olive oil, gelatin,lactose, terra alba, sucrose, dextrin, magnesium carbonate, sugar,cyclodextrin, amylose, magnesium stearate, talc, gelatin, agar, pectin,acacia, stearic acid or lower alkyl ethers of cellulose, silicic acid,fatty acids, fatty acid amines, fatty acid monoglycerides anddiglycerides, pentaerythritol fatty acid esters, polyoxyethylene,hydroxymethylcellulose and polyvinylpyrrolidone. Similarly, the carrieror diluent can include any sustained release material known in the art,such as glyceryl monostearate or glyceryl distearate, alone or mixedwith a wax.

The formulations can be mixed with auxiliary agents which do notdeleteriously react with the active compounds. Such additives caninclude wetting agents, emulsifying and suspending agents, salt forinfluencing osmotic pressure, buffers and/or coloring substancespreserving agents, sweetening agents or flavoring agents. Thecompositions can also be sterilized if desired.

The route of administration can be any route which effectivelytransports the active compound of the invention which inhibits theactivity of the IRE1α to the appropriate or desired site of action, suchas oral, nasal, pulmonary, buccal, subdermal, intradermal, transdermalor parenteral, e.g., rectal, depot, subcutaneous, intravenous,intraurethral, intramuscular, intranasal, ophthalmic solution or anointment, the oral route being preferred.

For parenteral administration, the carrier will typically comprisesterile water, although other ingredients that aid solubility or serveas preservatives can also be included. Furthermore, injectablesuspensions can also be prepared, in which case appropriate liquidcarriers, suspending agents and the like can be employed.

For topical administration, the compounds of the present invention canbe formulated using bland, moisturizing bases such as ointments orcreams.

If a solid carrier is used for oral administration, the preparation canbe tableted, placed in a hard gelatin capsule in powder or pellet formor it can be in the form of a troche or lozenge. If a liquid carrier isused, the preparation can be in the form of a syrup, emulsion, softgelatin capsule or sterile injectable liquid such as an aqueous ornon-aqueous liquid suspension or solution.

Injectable dosage forms generally include aqueous suspensions or oilsuspensions which can be prepared using a suitable dispersant or wettingagent and a suspending agent Injectable forms can be in solution phaseor in the form of a suspension, which is prepared with a, solvent ordiluent. Acceptable solvents or vehicles include sterilized water,Ringer's solution, or an isotonic aqueous saline solution.Alternatively, sterile oils can be employed as solvents or suspendingagents. Preferably, the oil or fatty acid is non-volatile, includingnatural or synthetic oils, fatty acids, mono-, di- or tri-glycerides.

For injection, the formulation can also be a powder suitable forreconstitution with an appropriate solution as described above. Examplesof these include, but are not limited to, freeze dried, rotary dried orspray dried powders, amorphous powders, granules, precipitates, orparticulates. For injection, the formulations can optionally containstabilizers, pH modifiers, surfactants, bioavailability modifiers andcombinations of these. The compounds can be formulated for parenteraladministration by injection such as by bolus injection or continuousinfusion. A unit dosage form for injection can be in ampoules or inmulti-dose containers.

The formulations of the invention can be designed to provide quick,sustained, or delayed release of the active ingredient afteradministration to the patient by employing procedures well known in theart. Thus, the formulations can also be formulated for controlledrelease or for slow release.

Compositions contemplated by the present invention can include, forexample, micelles or liposomes, or some other encapsulated form, or canbe administered in an extended release form to provide a prolongedstorage and/or delivery effect. Therefore, the formulations can becompressed into pellets or cylinders and implanted intramuscularly orsubcutaneously as depot injections. Such implants can employ known inertmaterials such as silicones and biodegradable polymers, e.g.,polylactide-polyglycolide. Examples of other biodegradable polymersinclude poly(orthoesters) and poly (anhydrides).

For nasal administration, the preparation can contain a compound of theinvention which inhibits the enzymatic activity of the focal adhesionkinase, dissolved or suspended in a liquid carrier, preferably anaqueous earner, for aerosol application. The carrier can containadditives such as solubilizing agents, e.g., propylene glycol,surfactants, absorption enhancers such as lecithin (phosphatidylcholine)or cyclodextrin, or preservatives such as parabens.

For parenteral application, particularly suitable are injectablesolutions or suspensions, preferably aqueous solutions with the activecompound dissolved in polyhydroxylated castor oil.

Tablets, dragees, or capsules having talc and/or a carbohydrate carrieror binder or the like are particularly suitable for oral application.Preferable carriers for tablets, dragees, or capsules include lactose,corn starch, and/or potato starch. A syrup or elixir can be used incases where a sweetened vehicle can be employed.

A typical tablet that can be prepared by conventional tabletingtechniques can contain:

Core: Active compound (as free compound or salt thereof)  250 mgColloidal silicon dioxide (Aerosil) ®  1.5 mg Cellulose, microcryst.(Avicel) ®   70 mg Modified cellulose gum (Ac-Di-Sol) ®  7.5 mgMagnesium stearate Ad. Coating: HPMC approx.    9 mg *Mywacett 9-40 Tapprox.  0.9 mg *Acylated monoglyceride used as plasticizer for filmcoating.

A typical capsule for oral administration contains compounds of theinvention (250 mg), lactose (75 mg) and magnesium stearate (15 mg). Themixture is passed through a 60 mesh sieve and packed into a No. 1gelatin capsule. A typical injectable preparation is produced byaseptically placing 250 mg of compounds of the invention into a, vial,aseptically freeze-drying and sealing. For use, the contents of the vialare mixed with 2 mL of sterile physiological saline, to produce aninjectable preparation.

The compounds of the invention can be administered to a human in need ofsuch treatment, prevention, elimination, alleviation or amelioration ofa malcondition that is mediated through the action of IRE1α, forexample, cancer, neurodegenerative diseases, inflammation, metabolicdisorders, liver dysfunction, brain ischemia, or heart ischemia.

The pharmaceutical compositions and compounds of the present inventioncan generally be administered in the form of a dosage unit (e.g. tablet,capsule, etc.) in an amount from about 1 ng/kg of body weight to about0.5 g/kg of body weight, or from about 1μ/kg of body weight to about 500mg/kg of body weight, or from about 1μ/kg of body weight to about 250mg/kg of body weight, most preferably from about 20μ/kg of body weightto about 100 mg/kg of body weight. Those skilled in the art willrecognize that the particular quantity of pharmaceutical compositionand/or compounds of the present invention administered to an individualwill depend upon a number of factors including, without limitation, thebiological effect desired, the condition of the individual and theindividual's tolerance for the compound.

The compounds of the invention are effective over a wide dosage range.For example, in the treatment of adult humans, dosages from about 0.05to about 5000 mg, preferably from about 1 to about 2000 mg, and morepreferably between about 2 and about 2000 mg per day can be used. Atypical dosage is about 10 mg to about 1000 mg per day. In choosing aregimen for patients it can frequently be necessary to begin with ahigher dosage and when the condition is under control to reduce thedosage. The exact dosage will depend upon the activity of the compound,mode of administration, on the therapy desired, form in whichadministered, the subject to be treated and the body weight of thesubject to be treated, and the preference and experience of thephysician or veterinarian in charge. IRE1α inhibitor bioactivity of thecompounds of the invention can be determined by use of an in vitro assaysystem which measures the activity of IRE lot, which can be expressed asEC₅₀ or IC₅₀ values, as are well known in the art inhibitors of theinvention can be determined by the method described in the Examples.

Generally, the compounds of the invention are dispensed in unit dosageform including from about 0.05 mg to about 1000 mg of active ingredienttogether with a pharmaceutically acceptable carrier per unit dosage.

Usually, dosage forms suitable for oral, nasal, pulmonal or transdermaladministration include from about 125 μg to about 1250 mg, preferablyfrom about 250 μg to about 500 mg, and more preferably from about 2.5 mgto about 250 mg, of the compounds admixed with a pharmaceuticallyacceptable carrier or diluent.

Dosage forms can be administered daily, or more than once a day, such astwice or thrice daily. Alternatively dosage forms can be administeredless frequently than daily, such as every other day, or weekly, if foundto be advisable by a prescribing physician.

An embodiment of the invention also encompasses prodrugs of a compoundof the invention which on administration undergo chemical conversion bymetabolic or other physiological processes before becoming activepharmacological substances. Conversion by metabolic or otherphysiological processes includes without limitation enzymatic (e.g.,specific enzymatically catalyzed) and non-enzymatic (e.g., general orspecific acid or base induced) chemical transformation of the prodruginto the active pharmacological substance. In general, such prodrugswill be functional derivatives of a compound of the invention which arereadily convertible in vivo into a compound of the invention.Conventional procedures for the selection and preparation of suitableprodrug derivatives are described, for example, in Design of Prodrugs,ed. H. Bundgaard, Elsevier, 1985.

In another embodiment, there are provided methods of making acomposition of a compound described herein including formulating a,compound of the invention with a pharmaceutically acceptable carrier ordiluent. In some embodiments, the pharmaceutically acceptable earner ordiluent is suitable for oral administration. In some such embodiments,the methods can further include the step of formulating the compositioninto a tablet or capsule. In other embodiments, the pharmaceuticallyacceptable carrier or diluent is suitable for parenteral administration.In some such embodiments, the methods further include the step oflyophilizing the composition to form a lyophilized preparation.

The compounds of the invention can be used therapeutically incombination with i) one or more other IRE1α inhibitors and/or ii) one ormore other types of protein kinase inhibitors and/or one or more othertypes of therapeutic agents which can be administered orally in the samedosage form, in a separate oral dosage form (e.g., sequentially ornon-sequentially) or by injection together or separately (e.g.,sequentially or non-sequentially).

Accordingly, in another embodiment the invention provides combinations,comprising:

a) a compound of the invention as described herein; and

b) one or more compounds comprising:

-   -   i) other compounds of the present invention,    -   ii) other agents or medicaments adapted for treatment of a        disease or malcondition for which inhibition of IRE1α Is        medically indicated, for example, vitamin E, an antioxidant,        hydralazine, or any combination thereof. Such compounds, agents        or medicaments can be medically indicated for treatment of        cancers such as TNRC or ovarian cancer, neurodegenerative        diseases, inflammation, metabolic disorders, liver dysfunction,        autoimmune diseases, brain ischemia, or heart ischemia.

Combinations of the invention include mixtures of compounds from (a) and(b) in a single formulation and compounds from (a) and (b) as separateformulations. Some combinations of the invention can be packaged asseparate formulations in a kit. In some embodiments, two or morecompounds from (b) are formulated together while a compound of theinvention is formulated separately.

The dosages and formulations for the other agents to be employed, whereapplicable, will be as set out in the latest edition of the Physicians'Desk Reference, incorporated herein by reference.

The Examples illustrate some of experimental work performed in thedevelopment of the invention.

Example 1: Vitamin E and Hydrazine Suppress Lipid Accumulation inMyeloid Dendritic Cells

Consistently, both vitamin E and hydralazine suppressed pathologicalintracellular lipid accumulation in myeloid dendritic cells exposed toovarian cancer ascites supernatants (FIG. 1). Based on the strongevidence linking aberrant lipid accumulation myeloid cellimmunosuppression, these agents can be used to restore the function ofantigen presenting cells in the tumor microenvironment.

Example 2: FRET Assay

In addition to the indirect inhibitors vitamin E and hydralazine, thecompositions and methods described herein can include one or moredirect, small molecule IRE1α inhibitors.

IRE1α is a dual enzyme, containing a kinase and endoribonuclease domain.Phosphorylation of the kinase domain during times of ER stress leads toactivation of the endoribonuclease domain and subsequent Xbp1 splicing,indicating that small molecules designed to block either the kinasedomain or the endoribonuclease domain are feasible inhibitorystrategies.

To evaluate potential small molecule IRE1 inhibitors, a Forsterresonance energy transfer (FRET)-based small molecule IRE1 screeningsystem was used. In brief, a small XBP1-mimetic RNA hairpin containingsequence features required for IRE1α-mediated splicing has beensynthesized with the fluorophore 6FAM attached to the 5′ end and thequenching dye Black Hole Quencher 1 (BHQ1) attached to the 3′ end. Whenthe hairpin is intact, 6FAM fluorescence is completely absorbed by BHQ1;however, IRE1α-mediated cleavage of the RNA hairpin leads to an increasein the fluorescence signal. The inventors also incorporated a pointmutant version of this same RNA hairpin that is resistant toIRE1α-mediated cleavage to control for non-specific RNAse contamination(FIG. 2).

Example 3: Potent IRE1α Inhibitors Identified by FRET Assay

Approximately 170 compounds were obtained and evaluated using the FRETassay, and at least one active compound was identified from this screen(IC50: 26 μM, FIG. 3). Compound activity was evaluated at thebiotechnology company Cyclofluidic guided entirely by the inventors.

Example 4: Computational Screening

After establishing the FRET system, computational models of IRE1α basedon published crystal structures were used to dock over 7 millioncompounds commercially available from the company eMolecules. Dockingwas performed using the Schrodinger software suite.

The cytoplasmic domain of human IRE1α (approximately residues 465-977)has been crystallized five separate times (PDBs 4PL3, 4U6R, 4PL4, 4PL5,and 3P23) in different states of phosphorylation and activation, as wellas with both endoribonuclease inhibitors and kinase Inhibitors (Sancheset al., Nature Communications 5:4202 (2014); Harrington et ah, ACS MedChem Letters 6:68-72 (2015); All et al., The EMBO J 30:894-905 (2011)).These studies and others (see, e.g., Wang et al., Nature Chem Biol8:982-9 (2012)) provide substantial evidence that IRE1α kinaseinhibitors can either inhibit or activate the IRE1α endoribonucleasedomain depending on their binding mode.

Type I kinase inhibitors that lock the IRE1α kinase domain into a“DFG-out” conformation block endoribonuclease activity, while inhibitorsthat lock the kinase domain into a “DFG-in” conformation trigger mRNAsplicing despite abrogating autophosphorylation.

All known endoribonuclease inhibitors bind to a shallow pocket in ahighly solvent exposed manner at the IRE1α C-terminus, and make too fewkey binding contacts to effectively model computationally.

At the time this project was initiated, the only kinase inhibitorco-crystallized with IRE1α enforced a Type I, DFG-in configuration (PDB4U6R). To generate a model of IRE1α in the target Type II, DFG-outconfiguration, the inventors computationally grafted the DFG loop fromthe crystal structure of the SRC kinase bound to the type II inhibitor1-(4-(4-Amino-1-isopropyl-1H-pyrazolo[3,4-d]pyrimidin-3-yl)phenyl)-3-(3-(trifluoromethyl)phenyl)ureaonto the 4U6R IRE1 crystal structure, as this compound also inhibits theIRE1α kinase and endoribonuclease domains. After grafting the SRCDFG-loop onto the IRE1α crystal structure, the SRC inhibitor was dockedinto the hybrid model for quality control.

The SRC inhibitor exhibited a good docking score using unconstrainedrigid receptor docking, as its urea group made hydrogen bonds with botha serine residue N-terminal to the DFG loop and a lysine-aspartate saltbridge in the kinase active site. With the initial model validated, theset of all compounds commercially available from the company eMolecules(over 7 million in sum) was used as the screening collection. From thefull list of 7 million compounds, only urea and amide-containingstructures were computationally docked (˜800,000 compounds), as thesemotifs form key hydrogen bond interactions with kinase DFG loops. Topscoring compounds were clustered by structural similarity and filteredfor those with desirable properties, and the top scoring compounds fromeach of 49 clusters were ordered and tested by FRET assay.

Initial results indicated that one of the 49 compounds exhibited someactivity against IRE1. The structure-activity relationships of anadditional 62 compounds were examined. However, secondary screeningafter FRET assay optimization, performed at the CRO Cyclofluidic,revealed that none of these 111 compounds exerted any activity.Cyclofluidic had published a small set of approximately 50 compounds (5)from their internal work on derivatives of the BCR-ABL kinase inhibitorPonatinib, and the inventors also screened these published compounds forIRE1α inhibitory activity.

While optimizing the first compound series, new crystal structures ofIRE1α in complex with Type II, DFG-out-inducing kinase inhibitors becameavailable (Concha et al., Molecular Pharmacol 88:1011-2 (2015)), whichwas used to develop a second model of IRE1α.

First, the ponatinib-like compounds were docked into this new model,allowing some structural flexibility, to control for model quality.Subsequently, a second computational screen was performed with theupdated model, and compounds for follow up were selected as follows:

1. Docked into the ponatinib-like compound induced structure.

2. H-bond with hinge NH

3. Strained compounds removed

4. Any compound with similarity to any of the known compounds testedthus far removed

5. Clustering

6. Selecting the highest docking score per cluster

The top 63 compounds based on this strategy were then tested, and onlyone compound showed weak activity by FRET assay (FIG. 3).

Example 5: Design of Additional Compounds

New small molecule compounds were designed to inhibit the human IRE1αkinase domain. Multiple variants of the original compound series weredesigned and ranked by computational docking score using the softwareLiveDesign. High scoring compounds were synthesized and evaluatedbiochemically by the IRE1α FRET assay.

Example 6: In Vitro FRET Assay Protocol

In vitro FRET assay was performed to evaluate the ability of selectcompounds to inhibit IRE1, the results of which are summarized in thefollowing table.

To perform the in vitro FRET assay, 1× complete assay buffer (CAB; 1MDTT, 50 mM sodium citrate pH 7.15, 1 mM magnesium acetate, 0.02% Tween20) was used to dilute SignalChem IRE1α protein to a final concentrationof 2 nM. Selected compounds were serially diluted with DMSO in anon-binding black 384-well plate for a total of 15 μl in each well, 2 μlof the serially diluted compound or DMSO control were then added to newwells containing 98 μl of 1×CAB, for a total volume of 100 μl, 10 μl ofwhich were then transferred to wells of a new plate, 5 μl of the dilutedIRE1α was then added to each well, 5 μl of a 400 mM XBP1 RNA probe wasthen added to each well. Fluorescence was then read over 30 minutes inkinetic mode (485/515 nm). Two RNA probes were used, XBP1 wildtype(CAUGUCCGCAGCACAUG; SEQ ID NO: 1) which is able to be spliced by activeIRE1α or XBP1 mutant (CAUGUCCCCAGCACAUG; SEQ ID NO: 2) which is unableto be spliced. Each probe contained a 5′ 6-FAM modification and a 3′IOWA Black FQ modification.

A second FRET assay was performed to assess ATP-mediated inhibition. Inthis case, compounds and IRE1α were prepared and combined as discussedabove, with the addition of ATP up to 1 mM final concentration. Thismixture was incubated at room temperature for 60 minutes and then 5 μlof 400 nM XBP1 wildtype or mutant RNA probe was added. Plates were thenread over 30 minutes in kinetic mode (485/515 nm).

Compound Mean EC₅₀ Ref. No, (nM) 76 C 75 A 74 A 21 C 73 A 57 A 51;Formic Acid B 50; HCl B 72 C 49; TFA D 48; TFA B 71; TFA B 20 D 19 D 47D 70 D 69 D 68 D 46; TFA A 45; TFA B 67; TFA D 66; TFA D 65 D 64 D 63 D62 D 44 B 43 D 42 D 41 D 40 D 39 D 38 D 37 A 36 A 35 A 61 D 34; TFA B33; TFA B 32; TFA D 31; TFA B 18; TFA D 17; TFA D 16; TFA A 15; HCl D 14C 13 D 60 B 59 B 58; HCl D 57 B 56 D 30 D 30 A 12 B 11 B 10 B 9 A 8 A 29A 28 A 27 A 26; TFA A 55 B 7 B 54 A 53 D 6 D 25 B 24; TFA A 5 D 4 D 3 D23 B 2 B 22 A 1 A Note: Biochemical assay Mean EC₅₀ data are designatedwithin the following ranges: A: ≤5000 nM B: >5000 nM to ≤50000 nMC: >50000 nM to ≤100000 nM D: >100000 nM

REFERENCES

-   1. Wang, L., et al., Divergent allosteric control of the IRE1 alpha    endoribonuclease using kinase inhibitors. Nat Chem Biol, 2012,    8(12): p. 982-9.-   2. Harrington, P. E., et al., Unfolded Protein Response in Cancer:    IRE1alpha Inhibition by Selective Kinase Ligands Does Not Impair    Tumor Cell Viability: ACS Med Chem Lett, 2015, 6(1): p, 68-72.-   3. Concha, N. O., et al., Long-Range Inhibitor-Induced    Conformational Regulation of Human IRE1alpha Endoribonuclease    Activity. Mol Pharmacol, 2015. 88(6): p. 1011-23.-   4. Mendez, A. S., et al., Endoplasmic reticulum stress-independent    activation of unfolded protein response kinases by a small molecule    ATP-mimic. Elife, 2015. 4.-   5. Cross, B. C., et al., The molecular basis for selective    inhibition of unconventional mRNA splicing by an IRE1-binding small    molecule. Proc Natl Acad Sci USA, 2012. 109(15): p. E869-78.-   6. Tang, C. H., et al., Inhibition of ER stress-associated    IRE-1/XBP-1 pathway reduces leukemic cell survival. J Clin    Invest, 2014. 124(6): p. 2585-98.-   7. Volkmann, K., et al., Potent and selective inhibitors of the    inositol-requiring enzyme I endoribonuclease. J Biol Chem, 2011.    286(14): p. 12743-55.-   8. Papandreou, I., et al., Identification of an Ire1alpha,    endonuclease specific inhibitor with cytotoxic activity against    human multiple myeloma. Blood, 2011. 117(4): p. 1311-4.-   9. Mirmura, N., et al., Blockade of XBP1 splicing by inhibition of    IRE1alpha is a promising therapeutic option in multiple myeloma.    Blood, 2012. 119(24): p. 5772-81.-   10. Cubillos-Ruiz, J. R., et al., ER Stress Sensor XBP1 Controls    Anti-tumor Immunity by Disrupting Dendritic Cell Homeostasis.    Cell, 2015. 161(7): p. 1527-38,-   11. Desai, B., et al., Rapid discovery of a novel series of Abl    kinase inhibitors by application of an integrated microfluidic    synthesis and screening platform. J Med Client, 2013. 56(7): p.    3033-47.-   12. Sanches M, Duffy N M, Talukdar M, Thevakumaran N, Chiovitti D,    Canny M D, et al. Structure and mechanism of action of the    hydroxy-aryl-aldehyde class of IRE1 endoribonuclease inhibitors.    Nature communications, 2014; 5:4202.-   13. Harrington P E, Biswas K, Malwitz D, Tasker A S, Mohr C, Andrews    K L, et al. Unfolded Protein Response in Cancer: IRE1alpha    Inhibition by Selective Kinase Ligands Does Not Impair Tumor Cell    Viability. ACS medicinal chemistry letters, 2015; 6:68-72.-   14. Ali M M, Bagratuni T, Davenport E L, Nowak P R,    Silva-Santisteban M C, Hardcastle A, et al. Structure of the Ire1    autophosphorylation complex and implications far the unfolded    protein response. The EMBO journal, 2011; 30:894¬905.-   15. Wang L, Perera B G, Hari S B, Bbhatarai B, Backes B. J, Seeliger    M A, et al. Divergent allosteric control of the IRE1alpha    endoribonuclease using kinase inhibitors. Nature chemical biology,    2012; 8:982-9.-   16. Desai B, Dixon K, Farrant E, Feng Q, Gibson K R, van Hoorn W P,    et al. Rapid discovery of a novel series of Abl kinase inhibitors by    application of an integrated microfluidic synthesis and screening    platform. Journal of medicinal chemistry, 2013; 56:3033-47.-   17. Concha N O, Smallwood A, Bonnette W, Totoritis R, Zhang G,    Federowicz K, et al. Long-Range Inhibitor-Induced Conformational    Regulation of Human IRE1alpha Endoribonuclease Activity. Molecular    pharmacology. 2015; 88:1011-23.

All patents and publications referenced herein are hereby specificallyincorporated by reference to the same extent as if it had beenincorporated by reference in its entirety individually or set forthherein in its entirety. Applicants reserve the right to physicallyincorporate into this specification any and all materials andinformation from any such cited patents or publications.

Additional Embodiments

The following exemplary embodiments are provided, the numbering of whichis not to be construed as designating levels of importance:

Embodiment 1 provides a compound of formula I:

wherein:

-   -   A and B are separately each a heterocyclyl ring or a phenyl        group, where the A ring has x R₁ substituents;    -   C is phenyl or pyridinyl;    -   D is heterocyclyl ring;    -   linkage₁ is a single bond between A and B;    -   linkage₂ is a C₁-C₃ alkylamido, amidoalkyl, amino, urea,        alkylurea, or ureaalkyl with a first and second terminal atom;    -   y is an integer of 0-3, and when y is 0, the linkage between the        rings is a single bond;    -   x is an integer of 0-4;    -   v is an integer of 0-2;    -   R₁ substituents on the A ring are selected from amino,        optionally substituted C₁-C₄ alkyl, optionally substituted        ether, optionally substituted C₁-C₄ alkoxy, oxy, hydroxy,        —NH—SO₂-phenyl-(R₅), and cyano;    -   R₂ substituents on the B ring are selected from amino, and        optionally substituted C₁-C₄ alkyl;    -   R₃ substituents on the C ring are selected from halo, CF₃,        optionally substituted C₁-C₄ alkyl, and optionally substituted        heteroaryl; and    -   R₄ substituents on the D ring are selected from optionally        substituted C₁-C₄ alkyl, optionally substituted C₁-C₄ alkoxy,        (optionally substituted C₁-C₃ alkylene)-OH, hydroxy, optionally        substituted aryl, optionally substituted benzyl, and optionally        substituted benzaldehyde;    -   R₅ is halo; or a pharmaceutically acceptable salt thereof.

Embodiment 2 provides the compound of embodiment 1, where the A ring isheteroaromatic.

Embodiment 3 provides a, compound of any one of embodiments 1 or 2,where the A ring is a fusion of two rings.

Embodiment 4 provides a compound of any one of embodiments 1-3, wherethe A ring is indazole, imadazopyridine, imadazopyrazine,imadazopyridazine, pyrrolopyridine, hexaliydrothienopyrimidine,imidazole, pyrazole, pyrazine, pyridine, pyrimidine,phenylpyrimidinamine, quinoiinyl, isoquinolinyl, tetrahydroquinolinyl,and quinazolinyl.

Embodiment 5 provides a compound of any one of embodiments 1-4, wherethe A ring is selected from:

Embodiment 6 provides a compound of any one of embodiments 1-5, wherethe B ring is a single, non-fused ring.

Embodiment 7 provides a compound of embodiment 6, where the B ring is Bring is pyrazolyl, imidazoiyl, or triazolyl.

Embodiment 8 provides a compound of any one of embodiments 1-5, wherethe B ring is a fusion of two rings.

Embodiment 9 provides a compound of any one of embodiments 1-8, wherethe B ring is selected from:

Embodiment 10 provides a compound of any one of embodiments 1-9, whereinthe C ring is phenyl.

Embodiment 11 provides a compound of any one of embodiments 1-10,wherein the linkage₂ is selected from:

-   -   wherein a hydrogen atom on Ring B replaced by the first terminal        atom of linkage₂ and a hydrogen atom on Ring C is replaced by        the second terminal atom of linkage₂.

Embodiment 12 provides a compound of any one of embodiments 1-11,wherein the D ring is a heterocyclyl ring containing at least one Natom.

Embodiment 13 provides a compound of embodiment 12, wherein the D ringis piperidinyl, piperazinyl, or morpholinyl.

Embodiment 14 provides a compound of any one of embodiments 1-11,wherein D ring is selected from

Embodiment 15 provides a compound of any one of embodiments 1-14, wherethe R₁ substituents on the A ring are selected from amino and C₁-C₃alkyl.

Embodiment 16 provides a compound of any one of embodiments 1-15, wherethe R₁ substituents on the A ring are selected from —NH₂ and CH₃.

Embodiment 17 provides a compound of any one of embodiments 1-14, withx=0.

Embodiment 18 provides a compound of any one of embodiments 1-16, withx=1.

Embodiment 19 provides a compound of any one of embodiments 1-16, withx=2.

Embodiment 20 provides a compound of any one of embodiments 1-19, withx=0, 1 or 2 when the A ring is a fusion of two rings.

Embodiment 21 provides a compound of any one of embodiments 1-16, withx=1 or 2 when the A ring is a single, nonfused ring.

Embodiment 22 provides a compound of any one of embodiments 1-21,wherein the R₃ substituent on the C ring is CF₃.

Embodiment 23 provides a compound of any one of embodiments 1-22,wherein the R₄ substituents on the D ring are selected from CH₃,CH₃CHCH₃, CH₃CH(CH₂)CH₃, and CH₃CH₂CH₃OH.

Embodiment 24 provides a compound of formula Ia:

wherein,

-   -   A₁ is N, CH, or CR₁; A₂ is N, CH, or CR₁; A₃ is N, CH, or        CR_(t); A₄ is N, CH, or CR₁; A₅ is N, CH, or CR₁; A₆ is N, CH,        or CR₁; A₇ is N CH, or CR₁;    -   v is an integer of 0-2;    -   Each R₁ is NH₂ or OH; provided that the number of R₁ on the A        ring does not exceed 4;    -   B is selected from:

-   -   each R₂ is independently selected from H and optionally        substituted C₁-C₄ alkyl;    -   X₁ and X₂ are each independently CH₂ or NH; with the provision        that X₁ and X₂ are not each CH₂;    -   R₃ is selected from H, halo, CF₃, optionally substituted C₁-C₄        alkyl, and optionally-substituted heteroaryl;    -   D is heterocyclyl ring containing at least one N atom; and    -   each R₄ is selected from H, optionally substituted C₁-C₁ alkyl,        optionally substituted C₁-C₄ alkoxy, (optionally substituted        C₁-C₄ alkylene)-OH, hydroxy, optionally substituted aryl, and        optionally substituted benzyl; or    -   a pharmaceutically acceptable salt thereof.

Embodiment 25 provides a compound selected from any of the compounds inTables 1-4, the Examples, or pharmaceutically acceptable salts thereof.

Embodiment 26 provides a compound of any one of embodiments 1-25,pharmaceutically acceptable salts thereof, or any combination of suchcompounds or salts.

Embodiment 27 provides a compound of embodiment 26, further comprisingvitamin E, an antioxidant, hydralazine, or any combination thereof.

Embodiment 28 provides a method comprising administering the compositionof any one of embodiments 26 or 27 to a mammal.

Embodiment 29 provides a method of embodiment 28, wherein the mammal isin need of administration of the composition.

Embodiment 29 provides a method of any one of embodiments 28 or 29,wherein the mammal has cancer, a neurodegenerative disease,inflammation, a metabolic disorder, liver dysfunction, an autoimmunedisease, brain ischemia, or heart ischemia.

Embodiment 29 provides a method of any one of embodiments 28-30, whereinthe mammal has triple negative breast cancer or ovarian cancer.

Embodiment 30 provides a compound of any one of embodiments 1-25 for usein treating cancer.

Embodiment 31 provides a use of a compound of any one of embodiments1-25 in treating cancer.

The specific compositions and methods described herein arerepresentative, exemplary and not intended as limitations on the scopeof the invention. Other objects, aspects, and embodiments will occur tothose skilled in the art upon consideration of this specification, andare encompassed within the spirit of the invention as defined by thescope of the claims. It will be readily apparent to one skilled in theart that varying substitutions and modifications may be made to theinvention disclosed herein without departing from the scope and spiritof the invention. The terms and expressions that have been employed areused as terms of description and not of limitation, and there is nointent in the use of such terms and expressions to exclude anyequivalent of the features shown and described or portions thereof, butit is recognized that various modifications are possible within thescope of the invention as claimed. Thus, it will be understood thatalthough the present invention has been specifically disclosed byembodiments and optional features, modification and variation of theconcepts herein disclosed may be resorted to by those skilled in theart, and that such modifications and variations are considered to bewithin the scope of this invention as defined by the appended claims andstatements of the invention.

The invention illustratively described herein may be practiced in theabsence of any element or elements, or limitation or limitations, whichis not specifically disclosed herein as essential. The methods andprocesses illustratively described herein may be practiced in differingorders of steps, and the methods and processes are not necessarilyrestricted to the orders of steps indicated herein or in the claims.

As used herein and in the appended claims, the singular forms “a,” “an,”and “the” include plural reference unless the context clearly dictatesotherwise. Thus, for example, a reference to “a compound” or “acatalyst” or “a ligand” includes a plurality of such compounds,catalysts or ligands, and so forth. In this document, the term “or” isused to refer to a nonexclusive or, such that “A or B” includes “A butnot B,” “B but not A,” and “A and B,” unless otherwise indicated.

Under no circumstances may the patent be interpreted to be limited tothe specific examples or embodiments or methods specifically disclosedherein. Under no circumstances may the patent be interpreted to belimited by any statement made by any Examiner or any other official oremployee of the Patent and Trademark Office unless such statement isspecifically and without qualification or reservation expressly adoptedin a responsive waiting by Applicants.

The invention has been described broadly and genetically herein. Each ofthe narrower species and subgeneric groupings falling within the genericdisclosure also form part of the invention. This includes the genericdescription of the invention with a proviso or negative limitationremoving any subject matter from the genus, regardless of whether or notthe excised material is specifically recited herein. In addition, wherefeatures or aspects of the invention are described in terms of Markushgroups, those skilled in the art will recognize that the invention isalso thereby described in terms of any individual member or subgroup ofmembers of the Markush group.

The Abstract is provided to comply with 37 C.F.R. § 1.72(b) to allow thereader to quickly ascertain the nature and gist of the technicaldisclosure. The Abstract is submitted with the understanding that itwill not be used to interpret or limit the scope or meaning of theclaims.

While preferred embodiments of the present invention have been shown anddescribed herein, it will be obvious to those skilled in the art thatsuch embodiments are provided by way of example only. Numerousvariations, changes, and substitutions will now occur to those skilledin the art without departing from the invention. It should be understoodthat various alternatives to the embodiments of the invention describedherein may be employed in practicing the invention. It is intended thatthe following claims define the scope of the invention and that methodsand structures within the scope of these claims and their equivalents becovered thereby.

1. (canceled)
 2. A method of treating cancer comprising: administering to a subject in need thereof a therapeutically effective amount of a compound of formula Ia:

wherein, A₁ is N, CH, or CR₁; A₂ is N, CH, or CR₁; A₃ is N, CH, or CR_(t); A₄ is N, CH, or CR₁; A₅ is N, CH, or CR₁; A₆ is N, CH, or CR₁; A₇ is N, CH, or CR₁; v is an integer of 0-2; each R₁ is NH₂ or OH; provided that the number of R₁ on the A ring does not exceed 4; B is selected from:

each R₂ is independently selected from H and optionally substituted C₁-C₄ alkyl; X₁ and X₂ are each independently CH₂ or NH; with the provision that X₁ and X₂ are not each CH₂; R₃ is selected from H, halo, CF₃, optionally substituted C₁-C₄ alkyl, and optionally substituted heteroaryl; D is a heterocyclyl ring containing at least one N atom; and each R₄ is selected from H, optionally substituted C₁-C₄ alkyl, optionally substituted C₁-C₄ alkoxy, (optionally substituted C₁-C₄ alkylene)-OH, hydroxy, optionally substituted aryl, and optionally substituted benzyl; or a pharmaceutically acceptable salt thereof.
 3. The method of claim 2, wherein A₁ is CH or CR₁; A₂ is N; A₃ is CH or CR₁; A₄ is N, CH, or CR₁; A₅ is CH or CR₁; A₆ is CH or CR₁; and A₇ is CH or CR₁.
 4. The method of claim 2, wherein B is

and each R₂ is independently H or methyl.
 5. The method of claim 2, wherein R₃ is selected from H, halo, and CF₃.
 6. The method of claim 2, wherein D is selected from:


7. The method of claim 2, wherein v is 1; and R₄ is selected from H, optionally substituted C₁-C₄ alkyl, (optionally substituted C₁-C₄ alkylene)-OH, hydroxy, optionally substituted aryl, and optionally substituted benzyl.
 8. The method of claim 2, wherein the compound is


9. The method of claim 2, wherein the compound is


10. The method of claim 2, wherein the compound is


11. The method of claim 2, wherein the compound is a compound of formula Ib:


12. The method of claim 2, wherein the compound is a compound of formula Ic: 